Let’s keep in mind, many of the inquisitions were NOT set up, nor administered, nor condoned nor ordained, by the Catholic Church. The Spanish Inquisition in particular was a response by the King and Queen of Spain after they finally got rid of the Moores from Spain. For many years Muslims attacked and controlled a great deal of Spain. When the Spanish Monarchy finally threw the Muslims out of the country, the Spanish Inquisition was established to make sure that people were adhering to the Catholic faith. Because it was the official religion of Spain, and because they didn’t want any more Moores hiding out in Spain, to make sure all the Muslims were gone. It was a state-run inquisition, and state-run executions. Torturing and killing eastern orthodox christians were a part of that, but that was the responsibility of the state-run inquisition.
Most of the catholic church sponsored, and sanctioned inquisitions took place much earlier in the middle ages and did not result in the ludicrous numbers of deaths that are often quoted. I heard at one point the inquisitions killed more than the black plague, which is just plain wrong. The point of the catholic church sponsored inquisitions were to root out heresies and make sure people were truly catholic. There were few deaths, mostly just penances and corrections of faith. And as bad as it sounds today, no there wasn’t a freedom of religion in those days. Not because the Pope didn’t want people to be free to worship as they wanted, but because catholicism was the only christianity and the church’s job was to ensure that it was being practiced correctly.
Keep in mind, at this time there were no protestants. Catholicism was THE christian religion in Europe, and most of western europe was catholic. Catholicism was the state sponsored, official religion of most nations. As bad as it sounds today, there was no freedom of religion in most kingdoms, and you had to be catholic. Not because the church said so, but because the king and queen said so.
And also keep in mind, torture, burning at the stake, all that stuff was seen as normal back then. People were drawn and quartered, tortured, burned, hanged, etc etc for all kinds of crimes. Yes, it’s barbaric today, but we must keep in mind the historical context. And don’t forget, less than 100 years ago we were lynching black people in the US, killing Indians, and segregation was legal and state sponsored.