Should the Old Testament commands to destroy the Amalekites be taken literally or spiritualized?

We are not to rationalize or fictionalize anything in Scripture that gives us a narrative of a historical event; that is not our choice. When God told Saul to destroy the Amalekites, every man, woman, child, and animal, it happened, and there was a very good reason for it; God does not act arbitrarily. Saul actually disobeyed by sparing the sheep, and Samuel confronted him about the bleating he heard, and for that the kingdom was taken from him, because it represented a bigger disobedience. The pattern of spiritualizing hard passages, whether the conquest, Jonah and the great fish, the six-day creation, the Tower of Babel, or the flood, treats them as mere story-filler, and that is not how we interpret the word of God. Unless God himself signals that something is a parable, which he never does with these narratives, you have no right to say it did not really happen. Once you make yourself the judge of which historical events are too fantastic to believe, you have lost the whole point of Scripture, which is that Scripture judges us, not the other way around.