I'm completely on your side, Banana, but it takes a lot of effort to dispute and I just think it's going to side-track the discussion too much. I mentioned the crusades, and then wuf sais they were done in retaliation... well now I can assume he talks about the first one in what... 1090? Where they took back Jerusalem from the islamic invasion. Now first of all I'm not even sure if that's the one he's refering to, and if he is, at that point Jerusalem was under Islamic rule for over 400 years. That would be the equivalent in saying native americans would be right in taking back american main land... 200 years from now. But I don't know nearly enough about that to talk about it in any meaningful way.
Also saying scientific discovery was done in the name of god, and lots of good stuff has been funded by the church... that's also correct, but it's not like there was an alternative, and to speculate what could have been if there would have been is not very useful imo.