This is something that has driven me to much reflection as long as I've been thinking about it with an adult brain (let's say 40+ years) --- and the problem is that to leave the Amalekite problem at that (as summarized above) is to ignore the actual moral theology which Christ teaches us through the Church. (That is, Catholicism: other churches, especially fundamentalist ones, may not agree: but I speak for Catholicism, not fundamentalism.)
I'll avoid pages of god-talkative cutting and pasting. Let me just point out that "gradual revelation" and the "development of doctrine" are both basic, foundational principles which you have, I think, failed to take into account.
It can be found, strikingly, in the six great “contradictions” set out by Jesus himself in Matthew 5: “You have heard it said… but I say unto you…”
Jesus rejects a specimen-preserved-in-amber view of Scripture and gives us instead, living Truth: not just that he “gives us” the interpretation of Scripture, but that He “is” the interpretation of Scripture.
What can one say about the eradication of the Amalekites vs the 20+ Old Testament verses in which God says He “hates” and “forbids” the shedding of innocent blood? What can one say about that pathetic scene in Judges when Jephthah sacrifices his daughter to fulfill a vow to the Lord, vs the many verses in which the Lord says that He detests child sacrifice and considers it an abomination? You say in the spirit of truth: if anyone thinks baby-killing and child-sacrifice are the positive will of God, they are wrong.
Alas, history is what it is, and it says in that same book of Judges, “Every man did what was right in his own eyes,”—this underlines the many-centuries-long tension between Biblical narrative and Divine law.
Bottom line, any honest inquirer must strive to understand the gradual nature of Biblical revelation and development of doctrine: this is indispensible in considering the relationship of the Old Testament and the New.
lj: interested in your view of mine at #81.