Why would God through Samuel tell Saul to "kill... even their babies"? 1 Samuel 15:3 CEV 1 One day, Samuel told Saul: The LORD told me to choose you to be king of his people, Israel. Now listen to this message from the LORD: 2 “When the Israelites were on their way out of Egypt, the nation of Amalek attacked them. I am the LORD All-Powerful, and now I am going to make Amalek pay! 3“Go and attack the Amalekites! Destroy them and all their possessions. Don't have any pity. Kill their men, women, children, and even their babies. Slaughter their cattle, sheep, camels, and donkeys.”
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As difficult as this command may be to understand, I would say, first, that none of us (including Christians, and even infants) are truly "innocent" in the eyes of God. We are all born with a sin nature, and justly deserve nothing but God's wrath and punishment. It is only by His grace (undeserved favor) and mercy that any of us are saved. The Amalekites had also afflicted Israel in their journey from Egypt to Canaan (as noted by Samuel in 1 Samuel 15:2), so they were not without guilt in the situation. In fact, God had already sworn that He would totally destroy the Amalekites for this action (Exodus 17:14). There is no indication that the Amalekites turned to God in any way during the long interval between that time and the events in 1 Samuel 15. God also (unlike us) knows the future. Had the infants been spared, it is fair (in my opinion) to speculate that they would have grown up not only to adopt the truly evil religious beliefs and practices of their parents, but also to be enemies of God's chosen people Israel, through whom the Messiah was to be born, and whose birth and bloodline it was necessary to preserve and protect at all costs for the sake of all humanity.
In case you feel your question hasn't been satisfied I have found some other people who have answered it, and I will just echo their comments here: PROBLEM: God is depicted in the Bible as a God of mercy and compassion, freely forgiving those who turn to Him (Ps. 94:18–19; Lam. 3:22; James. 5:11; 2 Peter 3:9). By vivid contrast, this text informs us that God commanded the seemingly merciless slaughter of innocent Amalekites—men, women, and children. Why? SOLUTION: The Amalekites were far from innocent. In fact, they were utterly depraved. What is more, they desired to destroy Israel (v. 2), God’s chosen people, the channel of His redemptive plans for all humankind (Gen. 12:1–3). The act of their total destruction was necessitated by the gravity of their sin. Otherwise, some hard-core remnant might rise to resume their hateful act toward God’s people and plan. As to the question about the innocent children, several observations are relevant. First, we are all born in sin (Ps. 51:5) and deserve death (Rom. 5:12). Everyone will eventually be taken by God in death—it is only a matter of when (Heb. 9:27). Second, God is sovereign over life and reserves the right to take it when He will (Deut. 32:39; Job 1:21). Third, all children who die before the age of accountability are saved (2 Sam. 12:23). Hence, the act by which God took the children is far from merciless.
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