Last week, a co-worker was reading Deuteronomy 20. He came to me with an important question: Why did God command the Israelites to completely destroy some nations?
This is my attempt to deal with this difficult question. (And I acknowledge that my response may not be completely adequate, but at this time, it's my best response.)
As the text states, the Israelites were commanded to completely destroy some nations as they were entering the Promised Land so that "they may not teach you to do according to all their abominable practices that they have done for their gods, and so you sin against the LORD your God" (Deuteronomy 20:18). Leviticus 18 describes the total corruption of these societies. They tolerated and practiced incest, fornication, adultery, homosexuality, bestiality, and child sacrifice in service to their false gods. Evil was celebrated. Selfishness, brutality, and narcissism ruled the land.
"(W)hen God directed the Children of Israel to go in and conquer the Promised Land, He told them to destroy the peoples who lived there. This command was necessary because of the vileness of the pagan religions practiced in that good land. The most brutal worship of all was that demanded by Moloch. This cruel demon was represented by an iron idol with hollow belly and with both arms bent in front in a cradling position. A fire was built in the hollow belly, and each mother was required to sacrifice her first-born by placing him in the idol's arms to be burned alive. During this horrible ceremony, the priests and priestesses of Moloch beat drums which reached a deafening crescendo as the mother laid her baby in the idol's arms. The purpose, of course, was to keep the mother from hearing her baby's screams" (Drums of Moloch, Herbert C. Casteel, pp. 94-95).
Two factors made matters worse for the inhabitants of the Promised Land: 1. They had a knowledge of their sins and of the true God who expected better from them. 2. They had been given centuries to repent.
Like all people, they had a basic understanding of right and wrong. However, they chose to "suppress the truth" (Romans 1:18). "Though they know God's decree that those who practice such things deserve to die, they not only do them but give approval to those who practice them" (Romans 1:32).
Although easy to overlook, we should also recognize that the pagan nations were well aware of the Lord's judgment long before destruction came upon them. In fact, Balaam was an internationally-known prophet of the Lord from a pagan land (Numbers 22). The true God was known in lands far away from the Israelites; and they did not have exclusive access to his prophets. Furthermore, as Rahab the pagan prostitute testified before her city was destroyed, "I know that the LORD has given you the land, and that the fear of you has fallen upon us, and that all the inhabitants of the land melt away before you. For we have heard how the LORD dried up the water of the Red Sea before you when you came out of Egypt..." (Joshua 2:9-10). For at least 40 years, the people of Jericho knew that their judgment day was coming, but they expressed no interest in changing their ways as the people of Ninevah would several centuries later (Jonah 3:6-10).
In addition, it should be noted that the nations inhabiting the Promised Land were given 400 years to repent (Genesis 15:16; Deuteronomy 9:5). Their destruction came fairly quickly, but it was only after God had waited patiently for centuries for them to change their hearts.
Also, different rules of warfare existed against the nations within the Promised Land than against the nations outside those boundaries. The nations within the Promised Land faced total destruction (Deuteronomy 20:16-18). They were facing the judgment of God. More conventional standards of warfare applied to enemy nations outside the Promised Land (Deuteronomy 20:10-15).
Finally, it should be noted that God's grace was extended to individuals even as their societies faced total annihilation. The prostitute Rahab and her family found grace. They were spared from God's judgment because they placed their faith in God and followed the instructions that they were given (Joshua 2-3).