The flaw in your son’s reasoning is he is focused too much on the things of this world. What is the final fate of those killed? That is the question. This world is but a flash. Judging God based on what he does in it is not really prudent. After all, I would gladly give up this life if it meant I would spend an eternity with Him.
I had similar crises in faith when I was a new believer, btw.
I don’t have a problem with God taking lives - the closing of the Red Sea, the death of the first-born of Egypt - but for Him to make his people kill children, babies, the unborn in their mothers?
I had a dream where the Angel of Death reached into me and lifted out my unborn baby (did not come to pass with that baby) and the Angel was impersonal, only doing the job he had been sent to do and no pain, no harm came to the dream baby - she went from my womb to heaven. So the Angel of Death and the first born I can accept.
But Ameleks hardened in sin? What was their eternal fate? If baby Ameleks were slaughtered did they go to heaven since their whole tribe was so evil it must be wiped out? A little two year old Amalek seeing his whole family bleeding on the floor before he was dashed against the wall?
What of virgin girls of other tribes given a few weeks to mourn their slain families before they became concubines. We hate the Muslims for that.
God fed the Israelites 40 years in the desert. Why didn’t He turn the desert into a land of milk and honey, instead of sending the Israeites into the lands of others?
Again, God can take my life any time He wants - it is His to take. But to send someone to destroy me? That wrongs the one sent.