New Testament
The New Testament prescribes shunning heretics, not murder:
"If anyone comes to you and does not bring this doctrine, do not receive
him into your house nor greet him; for he who greets him shares in his
evil deeds." (2 John 1:10-11).
"Now I urge you, brethren, note those who cause divisions and offenses,
contrary to the doctrine which you learned, and avoid them." (Romans
16:17).
"Reject a divisive man after the first and second admonition, knowing
that such a person is warped and sinning, being self-condemned." (Titus
3:10-11).
This is common church discipline for those brothers not walking the walk:
“I wrote to you in my epistle not to keep company with sexually immoral
people. Yet I certainly did not mean with the sexually immoral people of
this world, or with the covetous, or extortioners, or idolaters, since
then you would need to go out of the world. But now I have written to you
not to keep company with anyone named a brother, who is sexually immoral,
or covetous, or an idolater, or a reviler, or a drunkard, or an extortioner—not
even to eat with such a person. For what have I to do with judging those
also who are outside? Do you not judge those who are inside? But those
who are outside God judges. Therefore 'put away from yourselves the evil
person.'” (1 Corinthians 5:9-13).

Early Church
The early church writers continued the New Testament emphasis:
"However, it is a fundamental human right, a privilege of nature,
that every man should worship according to his own convictions: one man’s
religion neither harms nor helps another man. It is assuredly no part of
religion to compel religion — to which free-will and not force should lead
us — the sacrificial victims even being required of a willing mind. You
will render no real service to your gods by compelling us to sacrifice.
For they can have no desire of offerings from the unwilling, unless they
are animated by a spirit of contention, which is a thing altogether undivine.
Accordingly the true God bestows His blessings alike on wicked men and
on His own elect; upon which account He has appointed an eternal judgment,
when both thankful and unthankful will have to stand before His bar."
(To Scapula, Tertullian, Chapter 2).
Refuting the pagan Celsus, Origen notes Christians could not, even if they
wished, reimpose the Mosaic law, being forbidden to strike their enemies:
"However, if we must refer briefly to the difference between the constitution
which was given to the Jews of old by Moses, and that which the Christians,
under the direction of Christ’s teaching, wish now to establish, we would
observe that it must be impossible for the legislation of Moses, taken
literally, to harmonize with the calling of the Gentiles, and with their
subjection to the Roman government; and on the other hand, it would be
impossible for the Jews to preserve their civil economy unchanged, supposing
that they should embrace the Gospel. For Christians could not slay their
enemies, or condemn to be burned or stoned, as Moses commands, those who
had broken the law, and were therefore condemned as deserving of these
punishments; since the Jews themselves, however desirous of carrying out
their law, are not able to inflict these punishments." (Origen, Against
Celsus, Book 7, Chapter 26)
Lactantius sings the swan-song of the early church era:
"There is no occasion for violence and injury, for religion cannot
be imposed by force; the matter must be carried on by words rather than
by blows, that the will may be affected. Let them unsheath the weapon of
their intellect; if their system is true, let it be asserted. We are prepared
to hear, if they teach; while they are silent, we certainly pay no credit
to them, as we do not yield to them even in their rage. Let them imitate
us in setting forth the system of the whole matter: for we do not entice,
as they say; but we teach, we prove, we show. And thus no one is detained
by us against his will, for he is unserviceable to God who is destitute
of faith and devotedness; and yet no one departs from us, since the truth
itself detains him...Torture and piety are widely different; nor is it
possible for truth to be united with violence, or justice with cruelty...For
religion is to be defended, not by putting to death, but by dying; not
by cruelty, but by patient endurance; not by guilt, but by good faith:
for the former; belong to evils, but the latter to goods; and it is necessary
for that which is good to have place in religion, and not that which is
evil. For if you wish to defend religion by bloodshed, and by tortures,
and by guilt, it will no longer be defended, but will be polluted and profaned.
For nothing is so much a matter of free-will as religion; in which, if
the mind of the worshipper is disinclined to it, religion is at once taken
away, and ceases to exist. The right method therefore is, that you defend
religion by patient endurance or by death; in which the preservation of
the faith is both pleasing to God Himself, and adds authority to religion."
(Lactantius, Divine Institutes, Book 5, 20).
Even as the emperor was violating it, Ossius enunciated the principle of
separation of church and state:
"Stop, I beg you, and remember that you are a mortal man: fear the
day of judgment and keep yourself pure for it. Do not intrude yourself
into the affairs of the church, and do not give us advice about these matters,
but rather receive instruction on them from us. God has given you kingship,
but has entrusted us with what belongs to the church. Just as the man who
tries to steal your position as emperor contradicts God who has placed
you there, so too you should be afraid of becoming guilty of a great offense
by putting the affairs of the church under your control. It is written:
'Render unto Caesar the things that are Caesar's, and unto God those that
are God's.' (Matthew 22.21). Hence neither do we have the right to rule
over the world nor do you, emperor, have the right to officiate in church.
(Hist. Ar. 44.6-8, quoted p. 175, Athanasius and Constantius, Timothy D.
Barnes).
Athanasius protested in favor of persuasion:
"But this modern and accursed heresy, when it is overthrown by argument, when it is cast down and covered with shame by the very Truth, forthwith endeavors to coerce by violence and stripes and imprisonment those whom it has been unable to persuade by argument, thereby acknowledging itself to be anything rather than godly. For it is the part of true godliness not to compel, but to persuade, as I said before. Thus our Lord Himself, not as employing force, but as offering to their free choice, has said to all, 'If any man will follow after Me,' and to His disciples, 'Will ye also go away?'" (Athanasius, 'History of the Arians,' Part VII, Section 67).

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Albigensian Crusade
Jesus gave a simple test for discerning His followers: "By this all will know that you
are My disciples, if you have love for one another." (John 13:35).
As far as is the east from the west is mass murder from "love for one another." Yet
mass murder, against the gnostic dualists of Southern France,
the Albigensians, is just what history has hid her weeping eyes
from seeing, instigated by the very institutions upon which the
Roman Catholic Church bases its claim to legitimacy:
"It was [Pope] Innocent III who initiated measures which dealt the decisive blows against the dissidents...The
outstanding lord in Southern France, Count Raymond VI of Toulouse,
evaded Papal efforts to induce him to take positive action and
Philip Augustus, the King of France, hesitated further to complicate
his own difficult problems, including his chronic troubles with
England, by risking a prolonged internal war to enforce the
Papal commands. Then, in 1208, the Papal Legate, Peter of Castelnau,
was murdered in Raymond's domains and perhaps at his court.
Innocent took advantage of the widespread horror evoked by the
crime to call forth a crusading army. Religious zeal represented
in an outstanding leader of the crusading armies, Simon de Montfort,
combined with quite secular motives, sectional jealousies, and
the desire of the nobles of Northern France to reduce the power
of the South and to profit by its wealth.
"Years of warfare followed, with wholesale destruction. It is said that when one of the
first cities to be taken, Beziers, was entered, and the Papal
Legate was asked whether the Catholics should be spared, the
latter, fearing that the heretics would feign orthodoxy to save
their lives, commanded: 'Kill them all, for God knows His own.'"
Steps the ecclesiastical council at Toulouse took, after the corpses were disposed of,
to eradicate the Albigensian heresy include:
"Among other measures, the council forbade
to the laity the possession of copies of the Bible, except the
Psalms and such passages as were in the breviary, and condemned
vernacular translations." (Kenneth Scott Latourette, A History
of Christianity, Volume I, pp. 456-457).
The casualties of this Papal Crusade numbered in the tens of thousands:
"The Church reserved to itself the right to redistribute among the
more faithful crusaders the confiscated lands of the defeated heretics.
Thus the crusade attracted the most disreputable elements in northern France,
and the result was horror. In 1209, Arnold Aimery exulted to the Pope that
the capture of Beziers had been 'miraculous'; and that the crusaders had
killed 15,000, 'showing mercy neither to order, nor age nor sex.' Prisoners
were mutilated, blinded, dragged at the hooves of horses and used for target
practice." (Paul Johnson, A History of Christianity, p. 252).
Can blame for this event be laid on Jesus' shoulders? No!:
"You have heard that it was said, 'An eye for an eye and a
tooth for a tooth.' But I tell you not to resist an evil person. But whoever slaps you on
your right cheek, turn the other to him also." (Matthew 5:38-39).

Waldensians
The Waldensians differed from the Albigensians in that the Waldensians
were orthodox, Bible-believing Christians. They are first heard from around
1170 A.D. as followers of a certain "Valdensius." Though not
gnostics, their experience with Rome was much the same:
"A fate similar to that of Pragelato [1487] was in store for the Waldensians in the valleys of Argentieres
and Vallouise. These folk had been consistently pacifist by tradition, so that they did not resist when the invaders came. The
crusaders then proceeded to level their villages, destroying every trace of the Waldensian heritage. A few escaped massacre by
hiding in caves or in wooded areas while others submitted to a forced adjuration of their faith. Those who managed to flee the
area eventually joined with the Waldensians in the far south of Italy." (Giorgio Tourn, The Waldensians, the first 800 years, p. 65).
Once the Protestant reformation got underway, these Christians reached
out to their reformed brethren. The end of their isolation did not guarantee
their safety but only marked them out the more for Rome's wrath:
"There were sporadic attempts at resistance by a few. The old tradition
of non-violence, however, with its innate respect for constituted authority,
its ingenuousness and simplicity of heart, led the Waldensians to give
themselves up. On June 5, 1561, the town of San Sisto, with its 6,000 inhabitants,
was burned to the ground. Guardia Piemontese, its neighbor, was likewise
destroyed. Prisoners were burned like torches, sold as slaves to the Moors
or condemned to die of starvation in the dungeons of Cosenza. The massacre
reached its height at Mantalto Uffugo on June 11th. On the steps in front
of the parish church, 88 Waldensians were slaughtered one by one, like
animals brought to market." (Giorgio Tourn, The Waldensians, the first
800 years, p. 91)
Surviving Waldensians adopted guerrilla tactics, and kept on surviving...and
being killed:
"On April 24 [1655], Pra del Torno was taken by assault, reduced to
rubble and thoroughly plundered -- that traditional place of refuge which
in the past had been the Waldensian bastion of resistance and sanctuary
of important victories. Within a few days the same fate befell Villar and
Bobbio. Soon the ghastly picture was everywhere the same -- unarmed people
tortured sadistically and massacred, the terror-stricken fleeing for their
lives while the soldiers came down from the heights laden with booty."
(Giorgio Tourn, The Waldensians, the first 800 years, p. 123).
Given that the victims of this unrelenting violence were Christians, it seems unduly harsh for atheists to nominate
its perpetrators as the true Christians.

What Went Wrong?
In the early church, bishops, including the bishop of Rome, were chosen
by vote of the clergy and laity: "The ordinary process of the choice
of a bishop by the middle of the third century was a nomination by the
other clergy, especially the presbyters, of the city; the approval of neighboring
bishops, and ratification or election by the congregation." (A History
of the Christian Church, Revised Edition, Williston Walker et al, p. 83).
Even Cyprian, an early promoter of clerical power, admits "the suffrage
of the people" was at that time considered requisite for the legitimate
election of a bishop:
"Moreover, Cornelius was made bishop by the judgment of God and of His Christ, by the testimony of almost all the clergy,
by the suffrage of the people who were then present, and by the assembly of ancient priests and good men..." (Cyprian, Letters, 51:8)
"...no one, after the divine judgment, after the suffrage of the people, after the consent of the co-bishops,
would make himself a judge, not now of the bishop, but of God." (Cyprian, Letters, 54:5)
"But — I speak to you as being provoked; I speak as grieving; I speak as constrained — when a bishop is appointed into
the place of one deceased, when he is chosen in time of peace by the suffrage of an entire people, when he is protected by the
help of God in persecution, faithfully linked with all his colleagues, approved to his people by now four years’ experience
in his episcopate...when such a one, dearest brother, is seen to be assailed
by some desperate and reckless men, and by those who have their place outside
the Church, it is manifest who assails him..." (Cyprian, Letters, 54:6)
"...while the Bishop Cornelius was ordained in the Catholic Church by the judgment of God, and by the suffrages of the clergy and people..." (Cyprian, Letters, 66:2).
"Which very thing, too, we observe to come from divine authority, that the priest should be chosen in the presence of the people under the eyes of all, and should be approved worthy and suitable by public judgment and testimony; as in the book of Numbers the Lord commanded Moses, saying, “Take Aaron thy brother, and Eleazar his son, and place them in the mount, in the presence of all the assembly, and strip Aaron of his garments, and put them upon Eleazar his son; and let Aaron die there, and be added to his people.” God commands a priest to be appointed in the presence of all the assembly; that is, He instructs and shows that the ordination of priests ought not to be solemnized except with the knowledge of the people standing near, that in the presence of the people either the crimes of the wicked may be disclosed, or the merits of the good may be declared, and the ordination, which shall have been examined by the suffrage and judgment of all, may be just and legitimate. And this is subsequently observed, according to divine instruction, in the Acts of the Apostles, when Peter speaks to the people of ordaining an apostle in the place of Judas. “Peter,” it says, “stood up in the midst of the disciples, and the multitude were in one place.” Neither do we observe that this was regarded by the apostles only in the ordinations of bishops and priests, but also in those of deacons, of which matter itself also it is written in their Acts: “And they twelve called together,” it says, “the whole congregation of the disciples, and said to them;” which was done so diligently and carefully, with the calling together of the whole of the people, surely for this reason, that no unworthy person might creep into the ministry of the altar, or to the office of a priest. For that unworthy persons are sometimes ordained, not according to the will of God, but according to human presumption, and that those things which do not come of a legitimate and righteous ordination are displeasing to God, God Himself manifests by Hosea the prophet, saying, “They have set up for themselves a king, but not by me.” For which reason you must diligently observe and keep the practice delivered from divine tradition and apostolic observance, which is also maintained among us, and almost throughout all the provinces; that for the proper celebration of ordinations all the neighboring bishops of the same province should assemble with that people for which a prelate is ordained. And the bishop should be chosen in the presence of the people, who have most fully known the life of each one, and have looked into the doings of each one as respects his habitual conduct. And this also, we see, was done by you in the ordination of our colleague Sabinus; so that, by the suffrage of the whole brotherhood, and by the sentence of the bishops who had assembled in their presence,
and who had written letters to you concerning him, the episcopate was conferred
upon him, and hands were imposed on him in the place of Basilides."
(Cyprian, Letters, 67:4-5).
The people were free to choose the person they wanted to govern the church;
they did not have to choose between candidates nominated by others. Just
as William Jennings Bryan's barn-burner of a speech, 'The Cross of Gold,'
inspired the Democratic National Convention to name him as their candidate
in 1896, Ambrose's speech led the church of Milan to elect him, though
he had not previously been mentioned as a candidate:
"So he went to the church. And when he was addressing the people, the voice of a child among the people is said to have called out suddenly: 'Ambrose bishop.' At the sound of this voice, the mouths of all the people joined in the cry: 'Ambrose bishop.' Thus, those who a while before were disagreeing most violently, because both the Arians and the Catholics wished the other side to be defeated and their own candidate to be consecrated bishop, suddenly agreed on this one with miraculous and unbelievable harmony." (Life of Ambrose, by Paulinus, Chapter 3).
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