One could also say that since I am a Protestant and all of the above attrocities were commited by the Catholic Church they haven't anything to do with me either.
Anyway, to re-state the above point, when someone acts in a manner contrary to the teachings or rules of a group or organisation that they claim to belong to, you can't blaim the organisation's teachings for their actions.
Clearly any sane human being would not approve of the Inquisition or the Crusades, though in the case of the Crusades you're applying today's standards to an entirely different world where warfare was commonplace.
I pointed out first that the main source of Christian teaching, the Bible, doesn't say anything about Crusades or Inquisitions. It's quite true that I don't need it not to engage in Crusades or Inquisitions, because it doesn't mention them! Even if it did not say, "Thou shall not kill" I would not kill someone, either.
You correctly point out that Atheism is different again in that it isn't any ideology or set of beliefs or values other than the non-existence of any gods. So the two genocidal atheists I mentioned don't have anything in common with yourselves.
To use another, non-religious example, if a member of the Liberal party commits murder, are Liberals pro-murder? (don't start) Clearly secular law states that murder is illegal. That person is going against established laws. If such a thing happened, clearly other members of the Liberal party would condemn his actions as loudly, or even more loudly than other people.
Further, in both the time of the Crusades and the early stages of the Inquisition (13th century), it's true that the Catholic Church had almost absolute political power in Europe and could cause or allow these events to happen.
One aspect of Christianity that is fortunate for the world (considering there are over 2 billion Christians) is its ability to reform; now I could copy+paste the entire history of the Protestant movement, reformation and subsequent Enlightenment age, but you probably already know about it.
There is no way an Inquisition or Crusade could occur today, or ever again in the forseeable future. Unforunately we still have a tiny minority of fanatics such as Abortion clinic bombers. I know parts of the USA have problems with lack of church/state separation. But compare our progress to say, Islam in the Middle East and... no comment.
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That quote: You should mention it was George HW Bush who said it. I'd also like to see what context it was said in, but Google can only find atheist sites using it alone with no context given. Examples of discrimination against atheists in the constitution would be even better.