Where's the data to support this claim? You do understand there were the crusades and all the violence out of that. (Don't get me started on the wars actually talked about in the bible as well, where god says from Deuteronomy 20:14
"As for the women, the children, the livestock and everything else in the city, you may take these as plunder for yourselves. And you may use the plunder the Lord your God gives you from your enemies." So basically he gave the warriors clearance to rape and pillage.)
The crusades are probably smaller, both in absolute terms and as a proportion of world population, than you realized.
I'm not sure how many of those events you can officially put down to atheism, but the death toll from officially atheist states alone--e.g., the USSR--are pretty bad. My reading is that religiously motivated manmade disasters are a blip compared to the secularly motivated ones. Your reading may vary, though. :)