Social darwinism doesn't really have anything to do with atheism, first of all. One can obviously be an atheist without being a social darwinist, and one can be a social darwinist without being an atheist. Even then, though, exactly how many people have social darwinists killed? Even in the heyday of eugenics, sterilisation was the method they used. There has not, to my knowledge, ever been any genocide perpetrated because of someone's social darwinism. Yes, a certain amount of social darwinist justification might exist (in the sense of "this race is genetically inferior"), but the underlying causes completely separate, and I think it'd be difficult to find a genocide that wouldn't have happened had the perpetrators not espoused those sorts of ideas.
The thing about not viewing people as having intrinsic worth is that if you're killing them, you probably don't believe that anyway, regardless of any religious beliefs. Sure, Christians and Muslims are taught that all people have intrinsic worth, but those passages are right next to the ones telling you to stone the gays. Some religious people might believe that every life truly is sacred, but in general, religious people are just as capable of deciding that lives don't have any value. Further, the
worst
viewpoint possible from atheism is really just neutral - that it doesn't matter if you kill someone. I have trouble thinking of an atheist justification for believing that someone is intrisically
bad
, that is, that their lives actually have a
negative
intrinsic value. There are plenty of examples of this sort of thinking among the religious.
Hitler was a devout Catholic until his death. It's kind of difficult to hate the Jews if you believe that they're the same as everybody else. I'm not really sure where this idea that Hitler was an atheist came from, but it's pretty easy to see from Hitler's speeches and
Mein Kampf
that he believed the Holocaust was "the Lord's work".
Machiavelli was a Catholic, too, but I'm sure you knew that. And yes, some atheists do believe that monstrous selfishness is a good thing (*coughaynrandcough*), but even they don't generally go around promoting genocide.
[color=darkblue]If there's anything more important than my ego around, I want it caught and shot now.[/color]