I'm confused. Did Dawkins say no war, or not as much war?
If he said the latter, their satire was off. Of course, it's not really possible to test his hypothesis, but it seems reasonable... certainly not deserving of being roasted by a two-part episode.
If it was the former, I'm surprised; I wouldn't agree with him there, and feel the satire would be warranted.
I got the sense while watching it they figured since they had poked fun of all religions, these atheists deserved to be next, as The God Delusion & Hitchen's as a speaker were popular right then. They picked on the highest profile guy at the time (Dawkins, although I think Hitchens or that creep Sam Harris are more deserving targets), but realized "Oh... maybe he's not that bad" after reading his book, and downplayed his involvement in the 2nd episode, which was... convoluted from what I remember.