St. Thomas Aquinas's view on "Whether heretics ought to be tolerated?"
St. Thomas Aquinas's Summa Theologica II-II q. 11 a. 3 c., his answer to the question "Whether heretics ought to be tolerated?," shows that although heretics deserve death, the Church must show them mercy, and if they are stubborn, apply disciplinary means like excommunication, only handing them over to the State for capital punishment as a last resort.
With regard to heretics two points must be observed: one, on their own side; the other, on the side of the Church. On their own side there is the sin, whereby they deserve not only to be separated from the Church by excommunication, but also to be severed from the world by death. For it is a much graver matter to corrupt the faith which quickens the soul, than to forge money, which supports temporal life. Wherefore if forgers of money and other evil-doers are forthwith condemned to death by the secular authority, much more reason is there for heretics, as soon as they are convicted of heresy, to be not only excommunicated but even put to death.
However, he advocates mercy; he continues:
On the part of the Church, however, there is mercy which looks to the conversion of the wanderer, wherefore she condemns not at once, but "after the first and second admonition," as the Apostle directs: after that, if he is yet stubborn, the Church no longer hoping for his conversion, looks to the salvation of others, by excommunicating him and separating him from the Church, and furthermore delivers him to the secular tribunal to be exterminated thereby from the world by death [as a last resort]. For Jerome commenting on Gal. 5:9, "A little leaven," says: "Cut off the decayed flesh, expel the mangy sheep from the fold, lest the whole house, the whole paste, the whole body, the whole flock, burn, perish, rot, die. Arius was but one spark in Alexandria, but as that spark was not at once put out, the whole earth was laid waste by its flame."
Answering the Asker's Questions
I have never encountered a Protestant leader who believed at any point in history that the church should take up arms, acting as a sort of temporary civil power, and engage in military conflict or apply the death penalty to heretics.
The Church during the Inquisition never executed heretics, but rather urged for their conversion, as the "Inquisition" Catholic Encyclopedia article shows. The Church simply pronounced them heretics; the State, who trusted the Church's judgment, oftentimes performed capital punishment on them because the State saw heretics as a threat to civil order.
I'm sure there might be some odd exception to the rule but in general Protestant churches hold separation of church and sate.
Protestants don't even believe in the visibility of the Church.
Where there may have been any direct official church involvment in any such action in old Lutherand or Anglican or whaever churches, Protetsants in genral would unanomously denounce those actions as the church is seprated from state functions.
And yet the Protestant revolt led to much bloodshed (e.g., the 30 Years' War).
Some Protestants think it's ok as a 'citizen' to support the government on civil grounds to war or even to apply the death penalty, but not as a church. At least this is the most common Protetsant view.
You might be confusing separation of Church and State (which is a heresy, condemned, e.g., in Popes Gregory VI's Mirari Vos §20 and Pius IX's Syllabus of Errors §65) from the distinction between Church and State, which has always been held (cf. Pope Leo XII's encyclical "On the origin of civil power," Diuturnum*), even during the Catholic Middle Ages, when Church and State were very close.
*cf. also Pope Leo XIII's encyclical on marriage, Arcanum Divinæ §36, for a description of the distinction between Church and State, how they are two separate "spheres":
Yet, no one doubts that Jesus Christ, the Founder of the Church, willed her sacred power to be distinct from the civil power, and each power to be free and unshackled in its own sphere: with this condition, however - a condition good for both, and of advantage to all men - that union and concord should be maintained between them; and that on those questions which are, though in different ways, of common right and authority, the power to which secular matters have been entrusted should happily and becomingly depend on the other power which has in its charge the interests of heaven.
However I was surprised when I looked up the Catholic Encyclopedia on the Inquisition. It more are less describes it as something that was necessary for the church to do at the time and does not seem to be opposed to that period when Popes lead military conflicts and applied death penalties to perceived heretical Christians. Even as they took the clear lead.
Read the "Crusades" Catholic Encyclopedia article. The crusades were defensive wars.
So it really leaves me wondering. Does the Catholic Church still think such a thing is OK? Is it OK that at times in history or potentially the future Catholics will bear the sword and become a civil power rather then a spiritual one only?
Why does defending oneself make oneself a civil power? Just as killing in self-defense can be justified for a single Christian (cf. St. Thomas Aquinas's famous Summa Theologica II-II q. 64 a. 7 article where he outlines the principle of double-effect and its conditions), so can it be justified for a group of Christians.
Also, more recently, you would be interested in the Papal Zouaves of the 19th century, a multi-national army of 20,000 Catholic men who defended the Pope. See Charles Coulombe's The Pope's Legion: The Multinational Fighting Force That Defended the Vatican.
I really mean is it considered OK at times to 'take the clear lead' in commanding others to kill people, as they did when killing people through the crusades and bulls against perceived heretics. I do not mean merely Catholic citizens following their kings or government, but the 'command' of those kings or governments 'to kill'. Does the Catholic church separate church and state or assume it is a state with power to declare war and kill if it seems God's will?
According to the "Inquisition" article:
ideas of the first five
centuries may be summarized as follows:
St. Augustine (Epistle
100, n. 1), almost in
the name of the western
Church, says: "Corrigi
eos volumus, non necari, nec disciplinam circa eos negligi volumus,
nec suppliciis quibus digni sunt exerceri" — we wish them corrected,
not put to death; we
desire the triumph of (ecclesiastical) discipline, not the death
penalties that they deserve. St. John
substantially the same in the name of the Eastern
Church (Homily 46 on
Matthew, no. 1): "To
consign a heretic to
death is to commit an offence beyond
atonement"; and in the
next chapter he says that
God forbids their
execution, even as He forbids us to uproot cockle, but He does not
forbid us to repel them, to deprive them of free speech, or to
prohibit their assemblies. The help of the "secular arm" was therefore
not entirely rejected; on the contrary, as often as the
general or domestic, required it,
Christian rulers sought
to stem the evil by
appropriate measures. As late the seventh century St. Isidore of
Seville expresses similar
sentiments (Sententiarum, III, iv, nn. 4-6).
It's clear the Church sought mercy and conversion, not revenge (only God can avenge). The Church's supreme law and mission is the salvation of souls.
I always thought the whole world no longer approved of that but now am thinking maybe because Catholics can't admit Papal erros they are sort of stuck approving all those ugly things done in the past by their Popes but am not sure if my instincts are wrong. Maybe Catholics do oppose direct church involvement in killing others?
The Church does not oppose the death penalty justly enacted by the State, but the Church would rather heretics convert and not die unrepentant.
I really am curious to find a reliable answer on this. I would like to know if Protestants and Catholics generally have a different view.
The difference appears to come down to a difference in understanding what the Church is. Protestants don't believe in the visibility of the Church, which greatly affects their views of how the Church should relate to the state, whereas Catholics do believe the Church is visible.
Also, there are some good books on the Catholic Church and State doctrine: