Why did God command the Canaanites' extermination?
In Deuteronomy 7:1-2, the Bible teaches, "When the LORD your God brings you into the land that you are entering to take possession of it, and clears away many nations before you, the Hittites, the Girgashites, the Amorites, the Canaanites, the Perizzites, the Hivites, and the Jebusites, seven nations more numerous and mightier than you, and when the LORD your God gives them over to you, and you defeat them, then you must devote them to complete destruction." Why did God command the complete destruction of Israel's enemies?
One of the best references for why God commanded the destruction of the nations within the promised land is in 2 Kings 17:6–20, in the explanation to Israel and Judah as to why God was allowing (or commanding) their destruction as a nation. In short, Israel and Judah (as nations) had become as evil as the nations before them. The "gods" of the Amorites, Canaanites, etc., had engaged in child sacrifice, and multiple other perversions. They served Asherah and Baal, and graven images. Romans 1 talks in generalities about the unrighteousness of humanity, saying that we "exchanged the truth about God for a lie and worshiped and served the creature rather than the Creator" (verse 25) and that "although they knew God, they did not honor him as God or give thanks to him, but they became futile in their thinking, and their foolish hearts were darkened" (verse 21). So what is the big deal? Worshiping and serving idols will never lead to life, which is found in God alone (John 10:10; 14:6). Worshiping and serving self is not conducive to loving others. Not honoring God leads only to death. God's desire is that we seek Him in repentance and reliance upon Him, so that we may truly live and truly love others.
In the desert, when the Israelites left Egypt, God was preparing a people to follow Him, and to establish a society based upon justice and mercy (Micah 6:8). Just as God started anew with the flood and Noah's descendants, so, too, God was "starting anew" a nation set apart to worship Him. In order to set the nation apart, it needed to be purified and also free from ungodly influence.
With this backdrop, we can look further in Deuteronomy 7 for the rationale for God's seemingly violent command: "You shall not intermarry with them, giving your daughters to their sons or taking their daughters for your sons, for they would turn away your sons from following me, to serve other gods. Then the anger of the LORD would be kindled against you, and he would destroy you quickly" (Deuteronomy 7:3-4). Three clear reasons are offered.
First, allowing Israel's enemies to remain would cause their children to stop following the Lord and serve other gods instead. The Lord commanded that the Israelites worship Him and no other (Exodus 20:3). Allowing their enemies to live would lead to intermarriage resulting in families that worshiped other gods. The Lord chose to prevent this sin by fully removing those people who served other gods in this land. Note, however, that this was specific to the land of Israel, not to other lands.
Second, Deuteronomy 7 teaches that if Israel's enemies survived and led them to worship other gods, the anger of the Lord "would be kindled against you." The Israelites had witnessed God's anger against Pharaoh in Egypt as well as against many of the Israelites in the desert who had rebelled against Him. The Israelites' desire was to worship the Lord and to obey Him in order to bring joy to the Lord. If they kindled His anger, He would not bless them in the land as He had promised, but would judge them.
Third, Deuteronomy 7 predicts God would destroy the Israelites if they allowed their enemies to live in the land of Israel. The Canaanites and other enemies in Israel's land had worshiped other gods for more than the previous four hundred years. God was using Israel as part of His judgment against Israel's enemies. However, if Israel refused to obey God and remove these enemies, His judgment would come upon them as well.
Again, it is important to note that this was a specific command in the context of warring nations as part of God's promise to bring Israel into its Promised Land. Though it represents a graphic destruction of many people, the alternatives were to live with people who would lead the Israelites to serve other gods and bring judgment upon them or even Israel being defeated by these enemies, which would result in violent deaths of a similar nature among the Israelites.
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