Jesus wouldn't have approved of that and they where disobeying scripture. I would say any church that approve of it was not a real church and that the participants where unsaved at the time although they may have been saved latter. (Like Saul of Tarsus, aka Paul)
The Roman Catholic church which claims to be the only true church on the other hand has approved of murder among other unscriptural things. Even though genuine real Christians where persecuted and killed by the Roman Catholic church during and around the time of the inquisition (For believing what the Bible says about baptism , for translating, printing, having, or even quoting the Bible in the common tongues) we still have to deal with people blaming us for what the Roman Catholic church did.
And do you think that Roman Catholics and Protestants are the only ones involved here? There have been real Christians which have never been part of the Roman Catholic church during its existence (and no it's existence doesn't go back to Peter) since well before the reformation. I'm not protestant nor Roman Catholic, I'm Christian.
There where people in the Protestant Churches who discriminated and persecuted those who believed what scripture says about baptism, and other things as well.
I'm not saying that there are no real Christians in the Roman Catholic church however I am saying that it is not the true church and that it's teachings are false. I am also saying that those who participated in the inquisition and murdered people where not real Christians. (At the time of their participation at least. Some of them probably did get saved latter) Christians have to deal with the mistakes that unscriptural organization has made.
Only God can forgive sins.