I think you may need a history lesson. The Crusades were a product of warring empires in response to Islamic invasions a thousand years ago. Just as we don't hold Saudi Arabia responsible for Saladin's warmongering, there's no justification for holding today's Catholics responsible for events hundreds and hundreds of years in the past.

Of course, the Inquisition is not what you believe either: http://www.strangenotions.com/spanish-inquisition/. In summary of that source, "The Church executed no one."

The Church supported many scientists and kept alive literacy in Europe following the fall of Rome. Gregor Mendel, father of genetics, was a monk. Georges LeMaitre was a priest who created the idea of the Big Bang. The Galileo story was more nuanced than I think you realize, but even so, the modern Church has apologized for its actions: http://www.nytimes.com/1992/10/31/world/after-350-years-vatican-says-galileo-was-right-it-moves.html. Even the foremost Catholic university in the United States, Notre Dame, has a quote supporting evolution inscribed in the floor of its main science building.

Of course, none of that has anything to do with defending rapists, which is why this is an anomaly and you are categorically mistaken.

EDIT: Downvotes but no evidence-backed rebuttal. Ok then.