What was God teaching Israel when he commanded them to remove the Canaanites?
God was teaching that evil is contagious and must be thoroughly removed. The Canaanites had persisted in wickedness for nearly four hundred ninety years, so if Israel spared them, their immorality and abominations would infect and destroy Israel, and God would then have to deal with Israel.
Les explains that God had waited almost four hundred and ninety years from Abraham's call until Joshua led Israel in, giving the Canaanites time to turn from their iniquity. Instead, they went deeper into wickedness, immorality, and abominations. When their iniquity reached the full mark, God instructed Joshua and the children of Israel not to spare a one. The lesson is illustrated by good potatoes or apples: putting one half-rotten one among them soon makes the whole group rotten. God was teaching Israel that they had to remove the rot, because unless they did, it would infect them, destroy them, and then He would have to deal with them. As the context notes, that is exactly what happened.