The question for me is, does a system do the most good for the majority? And in the case of places with a heavy religious element, the answer is most certainly no. Saudi Arabia, for example has a long history of oppressing women. Now, these human rights abuses can be viewed from a sociological stand-point. If they are then we have to acknowledge that Sharia Law, which is influenced by Islam, which is informed by The Koran, is merely a means of running a society. As outside observers (still thinking from a socioligical perspective) we would have no right to judge what we don't understand. The goal would merely be to understand.
But we do judge, because we ask questions about the source, which is the Koran in this example. And while you might call Sharia Law a distortion or perhaps a perversion of Islam, there is an opposing argument that suggests this is a valid interpretation, and that it is theologically correct.
Regarding the countries run by atheists, I can only assume that you are speaking about the Soviet Union (and I might add here that not everyone in a position of power was an atheist). And I agree with you that they had a very bad record on human rights abuses. But atheism is not a belief, it is the absence of belief. Just because your leaders suddenly decide that religion is illegal, doesn't mean you will stop believing. The USSR made a grave mistake when it failed to recognize the religious element of its people, but, blaming atheism for the attrocities makes no sense. It wasn't their goal to be atheists, there was no atheist book telling them to kill certain people, they killed and committed attrocities for purely political reasons. Now that doesn't it make it okay, but, it's not the same.
Now regarding religious reasons for killing. You have already brought up the Crusades, Inquisitions, etc... Now I will be the first to admit that the Crusades, for example, were not fought solely on the grounds of religion. But they were in fact, sanctioned by it. It was a religious war supported by the representative of God. The Pope. So, by extension it was the will of God. And, if you are peasant feasting on tree bark (quite literally they did eat bark in some cases) and you are told by your lord that you must go to the Holy Land and wage war for God, you are not going to argue, you are going to go and fight for God. That doesn't make you a sociopath, that makes you a believer.
Even to this day, the world is negatively impacted with religion. It might be more subtle, but it hinders progress. Think of voting and be honest with yourself when I ask this question. How many people, do you think vote with their religious beliefs in mind? I read some numbers recently that suggest 76% of Americans call themselves Christians and 45% of that percentage consider themselves fundamentalists (meaning they believe that God created the world in six, twenty-four hour days, that Jonah was actually swallowed by a whale, etc... ). Now, when fundamentalist cast their ballots, how do you think they are going to vote? They are going to vote the way the think God wants them to vote (think anti-abortion, prayer in school, etc.... ). Is this an informed decision? No, it's religion screwing up the world, plain and simple.