The Crusades were instigated by the Pope, so they did have a religious cause. However, once the Crusaders had seen just how powerful and potentially devastating the Saracens were, that was when they started to really put a lot of effort into their attacks. If religion had remained the only cause, then the third crusade would most likely have been the last crusade, thanks to Saladin.
The Aztec Sacrificial Wars were also started religiously, but again, Aztec society could have suppoerted their sacrificial needs for centuries without a war. The Sacrificial Wars were primarily a way of expanding the empire with some kind of spiritual back-up so people would not oppose them.
And the Inquisition was truly backed by the superstition that Jews wish to conquer the financial world. While this could be viewed as religious, I certainly would not consider it as such.
And as for Science vs. Religion; I am in full support of Science. But when it comes right down to it I would much rather trust something which cannot be proved but will still be believed in 1,000 years; than something which can be "proved" but in less than a century will probably be treated as the stupidity of the past.
