The questions we must first ask in relation to our question:
If God is immoral, who sets the standard for morality?
What were the victims of such atrocities doing to deserve judgement?
Is it wrong for God to take life if He gives it without merit?
The 5th book of the Old Testament, Deuteronomy, details a very shocking area of scripture in which God seemingly commands His people to perform numerous genocides:
Completely destroy them—the Hittites, Amorites, Canaanites, Perizzites, Hivites, and Jebusites, just as the LORD your God has commanded you
This sits poorly with many unbelievers, who rush to claim that this is a display of how God cannot be loving or good. This falls apart when we question the origins of morality—is it from God or is it from humans? If it is from God, who are we to object to what is wrong or right?
Whether understood or not, it is widely agreed that morality is objective, meaning that we understand that there is an absolute standard in which murder is wrong and showing compassion is right. This transcends culture, and for those cultures that do endorse evil, for example murder, we see a process of dehumanisation to cope with the innate guilt attached to performing such evil (propaganda against Jews by the Nazis and "cleansing" rituals by cannibals).
If morality is objective, therefore, there must be an authority that dictates what is right and what is wrong. This must be God. Why? Because if morality were based on human authority, a man like Stalin would be no more right or wrong about morality than someone such as Mother Teresa.
What, then, made these groups so deserving of God’s wrath? Let’s take the Canaanites as an example of how God actually intervenes to stop evil:
The Canaanites had become disobedient to God, not simply through trivial disregard but by sacrificing their own children to an idol. The Bible and historians corroborate that the Canaanites worshipped a false idol called Molech, whom they would heat up to scorching temperatures before placing their babies into the idol’s arms to burn to death as a sacrifice. Is God immoral for putting an end to such an abhorrent practice?
We must also acknowledge that God's taking of life is not immoral. This is best explained through an analogy:
A man, in generosity, gives a stranger a puppy and instructs them to care for it. At first, they are thankful for the gift, but as time goes on, the man returns to find that the stranger has been actively abusing the puppy. Angered, the man decides to reclaim what he once gave because the stranger was disobedient and evil.
Is this not the right thing for the man to do?
Conclusion
Life is given as a free gift from God and, if used in a disobedient and abusive way, can be justly taken away at any time. As God is the moral lawgiver, He is also the judge. The practises by certain groups in the Old Testament far overstepped the lines God gave them, so passing judgement on such groups is by no means immoral; instead, it may just be the most moral thing that could be done.