The Calvinists, Anglicans, Lutherans, Puritans did that too.
And all were wrong to do that.
The One True Apostolic Church on earth contains within itself all sorts of sinners and knaves, and some of them obtain positions of responsibility.
Those who led the Inquisitions could think their actions were justified. The Bible itself records instances where God commanded that formal, legal inquiries—that is, inquisitions—be carried out to expose secret believers in false religions. In Deuteronomy 17:2–5, God said: “If there is found among you, within any of your towns which the Lord your God gives you, a man or woman who does what is evil in the sight of the Lord your God, in transgressing his covenant, and has gone and served other gods and worshiped them, or the sun or the moon or any of the host of heaven, which I have forbidden, and it is told you and you hear of it; then you shall inquire diligently, and if it is true and certain that such an abominable thing has been done in Israel, then you shall bring forth to your gates that man or woman who has done this evil thing, and you shall stone that man or woman to death with stones.”
It is clear that there were some Israelites who posed as believers in and keepers of the covenant with Yahweh, while inwardly they did not believe and secretly practiced false religions, and even tried to spread them (cf. Deut. 13:6–11). To protect the kingdom from such hidden heresy, these secret practitioners of false religions had to be rooted out and expelled from the community. This directive from the Lord applied even to whole cities that turned away from the true religion (Deut. 13:12–18). Like Israel, medieval Europe was a society of Christian kingdoms that were formally consecrated to the Lord Jesus Christ. It is therefore quite understandable that these Catholics would read their Bibles and conclude that for the good of their Christian society they, like the Israelites before them, “must purge the evil from the midst of you” (Deut. 13:5, 17:7, 12). Paul repeats this principle in 1 Corinthians 5:13.
These same texts were interpreted similarly by the first Protestants, who also tried to root out and punish those they regarded as heretics. Luther and Calvin both endorsed the right of the state to protect society by purging false religion. In fact, Calvin not only banished from Geneva those who did not share his views, he permitted and in some cases ordered others to be executed for “heresy” (e.g., Jacques Gouet, tortured and beheaded in 1547; and Michael Servetus, burned at the stake in 1553). In England and Ireland, Reformers engaged in their own ruthless inquisitions and executions. Thousands of English and Irish Catholics were put to death—many by being hanged, drawn, and quartered—for practicing the Catholic faith and refusing to become Protestant. An even greater number were forced to flee to the Continent. We point this out to show that both sides understood the Bible to require the use of penal sanctions to root out false religion from Christian society.
Even as recently as the 1990's, the reformed "dominionist" Calvinist crowd (Gary North and friends) said that "idolatry" ought to be a capital crime. Asked whether Catholics would qualify as idolaters subject to the death penalty, their response was "Maybe, we're not sure".