Unlike us, God knows the future. God knew what the results would be if Israel did not completely eradicate the Amalekites. If Israel did not carry out God’s orders, the Amalekites would come back to trouble the Israelites in the future. Saul claimed to have killed everyone but the Amalekite king Agag (
1 Samuel 15:20). Obviously, Saul was lying—just a couple of decades later, there were enough Amalekites to take David and his men’s families captive (
1 Samuel 30:1-2). After David and his men attacked the Amalekites and rescued their families, 400 Amalekites escaped. If Saul had fulfilled what God had commanded him, this never would have occurred. Several hundred years later, a descendant of Agag, Haman, tried to have the entire Jewish people exterminated (see the book of Esther). So, Saul’s incomplete obedience almost resulted in Israel’s destruction. God knew this would occur, so He ordered the extermination of the Amalekites ahead of time.
In regard to the Canaanites, God commanded, “In the cities of the nations the LORD your God is giving you as an inheritance, do not leave alive anything that breathes. Completely destroy them — the Hittites, Amorites, Canaanites, Perizzites, Hivites and Jebusites — as the LORD your God has commanded you. Otherwise, they will teach you to follow all the detestable things they do in worshiping their gods, and you will sin against the LORD your God” (
Deuteronomy 20:16-18). The Israelites failed in this mission as well, and exactly what God said would happen occurred (
Judges 2:1-3;
1 Kings 11:5;
14:24;
2 Kings 16:3-4). God did not order the extermination of these people to be cruel, but to prevent even greater evil from occurring in the future.
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