Your examples of religion remind me of what I was taught when I had to do my California mission project versus what my son learned when he did his. The version I was taught was how the Monks were doing the Native Americans a big favor by bringing them religion and everybody lived happily ever after. My son learned what was more the truth which is that the Native Americans weren't treated well and didn't like being forced to convert to Christianity and having their culture taken away from them.
The things that you are talking about happened under the "name of Christianity" but it doesn't mean that the people were real Christians (aka followers of Jesus Christ). Most of the people who did horrible things to other people (i.e., the Crusades, the inquistion, witch hunts, the Roman Persecution, the Holocaust, Hitler, etc) were following a sect or religious branch of Christiandom, but not Christianity as taught by Jesus Christ or his disciples in the Bible...and yes, there is a big difference.