I wasn't arguing that it was their atheism that they committed atrocities in the name of - rather that you don't need religion to commit atrocities. That article and, I think, your position are pursuing the same fallacy but in the opposite direction.
Hitler had his ideology, Stalin his manifestos etc - they all had their own, unique 'holy book' or similar that justified their crimes and it would be a mistake as you've said to somehow link them all as being from a common position.
And yet Hitchens and possibly you do the same thing in the opposite direction: despite the average ISIS member having as much in common as your, say, average US muslim as a nazi might have to a 1917-era russian communist (next to nothing) - you are arguing that their religion, not their idealogy is at fault.
You might argue that the various holy books of faiths cause a problem: for as much as the bible and the (far better written) quran espouse love and joy etc etc they both also include a fair amount of violence. But these books have been rewritten, multiple times, and are constantly being reinterpreted. Blaming the text for the actions of the reader seems harsh.
I guess ultimately the problem I have is that people who say religion is the problem and it should be banned seem to me to be worryingly similar to those that said computer games should be banned in the 90s. A very small amount of people committed atrocities, and all of a sudden it was the games 'promoting violence and hatred' that needed to be stopped, rather than people confronting the more nebulous and difficult issue of culture surrounding the criminals that made them more susceptible to hate and sociopathy.