Well what is not realized to many is that back then the Church had a lot a power and was actually considered superior to the state in some places. Going against the church was considered similar to treason. Much like going against the interests of the United States or any other country can be considered treason. The penalty for treason in the United States can be death. Also some people believe that there is torture going on by this country in places around the world.
And If you ask the Palestinians and Arabs they would tell you the Jews are not so innocent in the area of killing and torture.
If you go against a kingdom or a country your going to pay a heavy price. And doesn't the Bible say people who go against the kingdom of God are going to pay a heavy price. I'm not saying the actions of the Church were correct back then, but they believed they were protecting God's kingdom. Much like the US and Israel believe they are protecting their country (kingdom) by their tough and militaristic actions which includes much killing, and according to some --torture.