Flesh, I fail to see how "militant atheism" is in any way a viable solution...

Sure, atrocities are committed in the name of religion. But not all religious people commit atrocities. I've met some amazingly down to earth, creative and compassionate people, who consider themselves very religious. So obviously, the problem isn't religion but rather the same barbarism you were complaining about.
Why blame religion for barbarism? Why not simply blame the brutality?
Personally I feel the whole notion of "militant atheism" strikes a chord amazingly similar to that of any fundamentalist group. An expressed limitation on acceptable beliefs. In fact that's the exact opposite of siStarIndigo's thought of ignoring the differences and simply co-existing.

Because that's the bottom line, isn't it? Co-existence. Does it matter who's "right" and whose "wrong" as long as everyone is respected for their individual humanity?

In the battle for humanity, there are no winners without losers... But it doesn't need to be a contest. We can coexist. A way to live without exploitation. A way to be right in a way that doesn't make other ways wrong.

Just a thought I had...