It is illogical for atheists to question the moral commands of God for two primary reasons:
1) The Bible is clear that God is the one Who defines morality to start with. He says what is right, wrong, good and evil. And He, as the Creator of the world and of all life, also has complete ownership of all that He has created. If He chooses to end the life of some of His creation (which by the way is corrupt and evil by nature and is guilty of breaking His holy law) by His sovereign command, then He not only has the right to do so but is also entirely just in doing so. So it is illogical for a limited, fallible human creation of the unlimited, infallible God to question the moral law and judgments of the omniscient definer of morality.
2) If you are an atheist then you cannot believe in any kind of absolute, universal morality. Morality itself is nothing more than a social construct and is defined by society. Therefore there is no moral code that can be said to "right" or "wrong" and no moral code can be said to be better than any other moral code. How is it that you, as an atheist, can say that the actions of the Israelites were absolutely evil? If you are an atheist, there is no such thing as evil. So for you then to express moral outrage at the actions of God as described in the Bible is entirely illogical.
If you are an atheist, then you can neither define what moral "good" and "evil" are supposed to be with any kind of certainty, nor can you condemn the moral actions of anyone in the Bible, especially God, without both contradicting your own beliefs as an atheist and stealing from the Christian worldview of absolute, universal morality.
I should also add, that you yourself are guilty of breaking God's moral law and will be held accountable to Him one day. The only escape that you can possibly have is through the grace of Jesus Christ who will forgive all those who call upon Him for forgiveness. Repent of your sins and turn to him.
Ronald Christopher Troutman