According to some theologies, killing someone in infancy guarantees their eternal salvation. On the other hand, if the kid grows up, he might reach the age of accountability and refuse God's saving grace, which means they will be lost. Is this an argument for abortion and infanticide, on the grounds that it is the only truly foolproof method of evangelism available???
The rebuttal to this argument is often that humans shouldn't play God. But what does that do to the argument above that a good God would not order the death of the Amalekite children? You can't criticize God for playing God.
I would just point out that it could turn out that God's having people killed may give the people who are killed the best chance of salvation. If there is an eternal life, then it may be that God is aware of eternal consequences that humans are not. Of course, on the thesis that "a tree lies as it falls," the Amalekite adults would be ushered immediately into eternal damnation.
I do think the Amalekite case, and cases like it, are somewhat more complex than ordinary human cases of genocide or infanticide.
Also, we ought to reflect a little bit on the phrase "human beings shouldn't play God." Should a thoroughgoing utilitarian who believes in God be deterred by this argument?