Simple: they didn't kill IN THE NAME OF atheism. They killed to solidify power and gain control. Many of them happened to be atheists, but they didn't kill under the banner of their atheism. Many of them also happened to have mustaches or wear boots or smoke, but that isn't why they killed either. Atheism is another trait they may have had, but it wasn't the reason they did what they did--either in their own mind or as the guise and cover they used to justify and pursue their agenda.

It isn't that hard, actually.