I think we have pretty much the same opinion on this. Morality is separate from religion or atheism. Some religions have a good moral code, but morality itself comes from the person.
Blaming the attrocities in Stalin's Russia on atheism would be like blaming the war in Iraq on christianity. I wouldn't blame every atrocity on religion. But there are some things, like specific holy wars, or Jihads which are largely a religious issue. But they are mainly historical, when religion had more say (or a more open say) in politics.
I recognise that it's easy to attack the extremists. Richard Dawkins in his documentary interviewed Ted Haggard, a fellow who would certainly fit the description of extremist in Britain. However, before his fall, Ted Haggard was head of the National Association of Evangelicals, a 40 million strong organisation. Atheists tend to pitch their arguments against the massive fundamentalist movement in the US, ignoring the more moderate christians both in the UK and abroad. But that's because it's the fundamentalist movement which is so dangerous.