The Canaanites' religious and cultural rituals were more the focus of the conquest than the lives of the inhabitants. Idolatry rather than the populace was the issue.
God despised the Canaanite worship of Baal as an idol. Because they were unclean in His eyes, He commanded Joshua to lead the Israelites in killing every Canaanite pagan man, woman, kid, and animal. When one of Joshua's generals disobeyed this stringent order by saving the animals (perhaps under the impression that the Israelites could benefit from their use), Joshua immediately had him put to death.
Why did God punish the Canaanites by enslaving them in their own land?
God offered Israel a clear justification for the need to exterminate the Canaanites in Deuteronomy 20:18: "so they may not instruct you to do according to all their abominable practices that they have done for their gods, and you trespass against the LORD your God."
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