Counting the numbers of deaths on both sides of this argument is not in anyway a measure of morality. For many reasons:
1. "In the name of". Whilst it is true that some wars and persecutions have been carried out in the name of Christianity or islam or (insert religion here), it's clear that the main motivation has always been power, ownership and control with religion providing the excuse. On the atheist side, no wars have been carried out in its name but several totalitarian regimes lead by atheists have performed horrific genocidal acts. But again, this is the nature of power.
2. Quantum. Even if it was possible to add up the deaths on each side it would be meaningless without allowing for the efficiency of modern weaponry and population sizes. Deaths would need to be weighted averages proportioned over time. The absurdity of this calculation is evident when you consider what damage a few dirty nuclear bombs or a biological weapon could do in the USA in the hands of a few Islamic extremists.
3. You can't generalise to the particular. An individual atheist is as likely to kill as a Christian and equally capable of doing good. That's just a statement of the obvious. And, as has been asked several times but never rebutted "what moral act can a christian perform that an atheist can not?"
4. Time. Morality is not absolute - despite the claims of extremist Christians. Our attitude to death, torture, slavery, freedom, homosexuality, women, democracy etc has changed over time.
5. Developed Society. We have developed strong secular institutions that have largely replaced the religion regulation of bad behaviour, most notably the Law and by providing welfare services, education and health.
All these things have made the argument of who owns the moral high ground utterly redundant in modern societies.
I have one reservation. Some religious organisations are dangerous and morally corrupt. But we shouldn't judge all people who have religious beliefs by the light of their extremists.
Life, don't talk to me about life.