The problem with the atheist religion is that there is nothing within atheism that gives a reason for not blowing your neighbor to kingdom come if the mood strikes you. History shows us that in the body count of those nations which have adopted official atheism as their belief system--- the Communist states. It comes to over 100 million, as you will see on this 'Communist Body Count' page.
Just one small sample of official atheism's death toll is the Holodomor--- the murder by starvation of from 5-7 million Ukrainians by the Soviet regime. While under a Christian worldview this planned-starvation massacre is unthinkable because each person killed is an immortal soul with an immortal destiny, for an atheist, a human is a mere clever animal and if they are in the way of your cause, well, there are plenty more clever animals where they came from.
The answer to the murdery atheist state question, I believe, is this: when you are willing to be open about the possibility of a God and of eternal rewards and punishments, or when you are surrounded by people who are open to this, your behavior is modified in the direction of obeying the standard moral rules (which, apart from details, are mostly shared across cultures and religions).
When you have accepted atheism as the One True Religion, and you live in an atheist state where only the devotees of this religion are eligible for positions of power, you live in a milieu where the very idea divine retribution for evil deeds is considered absurd. Therefore, if you want to just DO AWAY with some people who are blocking your idea of progress, your only concern is 'will I be caught and punished by my government for this?' If the answer is no--- if your government approves the killing, or if you are Joseph Stalin and run the government--- there is no good reason not to do the killings you need to do to carry out your plan. You'd be a fool not to do it, if it would aid your regime.
The problem of atheist state mass-murder has a tiny echo in the wave of bad behavior--- vandalism, riots/'protests' and the like--- carried out by teen atheists (some of them, of course, college age and older.) Most of them will outgrow their teen atheism the way people usually outgrow teen Wicca. But in the meantime, when they are spending their time hanging with their teen-atheist buddies, they are likely to do some rather bad behavior because their world-view is feeding off any tendencies they have toward teen rebellion. The only solution is for law enforcement NOT to let young people (of any religion) off with just a 'slap on the wrist' when they get involved in violent 'peaceful protests' or commit acts of ideologically motivated vandalism.
Apologetics 3:15: Is God Necessary for Morality?