Alright, let me tackle the crusades here. What happened with the crusades is that catholic priests were "selling forgiveness". You see, in order to make an extra buck, the catholic church would go "Oh, donate 500$ to church X for forgiveness!" (There is absolutely NO justification for this in the Bible, by the way. The catholics teach good works is necessary to get into heaven, which is completely counter to the Bible's doctrine of grace, and the main reason I don't consider the catholic church Christianity.) Anyway, the way this ties into the crusades is that the bishops and stuff were saying "Go on the crusades, instant forgiveness, period!". And the people going on the crusades took that to mean that they could behave however they wanted without penalty, leading to all sorts of immorality and evil acts. So you see, the thought process and reasoning behind the atrocities of the crusades were from distinctly catholic, not Christian motives.
As a side note, I'm confused about the "atheism = lack of belief" thing. I always thought "atheism = belief there is no God", as that's how I've always seen the word used (for example, vs "agnostic", who isn't sure if there's a God.) Anwyay, if "atheism = lack of belief", two things.
1) How do you want me to judge atheism?
and
2) By that definition, Hitler and Stalin and such were still atheists, so I fail to see how this changes anything.