The truth is that more people were killed in the name of atheism in the last century than the sum total of all of the religion related deaths you can actually cite numbers for, which attests to the fact that religion has had an overall good impact on man's history.
Non-sequitor. It does not follow, that if religion killed fewer people than atheism, it must therefore have had an overall good impact on man's history.
Besides, we really don't have good data to work with: for instance, what kind of per capita killings are we talking about? There were a lot fewer people alive when religion was dominant, and the means to kill them were much more primitive. Give your average 4th century Christian fanatic, or your average 21st century Muslim fanatic, large populations to work on, with modern weapons and modern techniques of social control, and I think we'd see religion rapidly rival atheism in the body count.