Why did God command the destruction of Canaan?

Because after four centuries of warning and patience the wickedness of the Canaanites finally reached the point God had said it would reach. The conquest was His judicial sentence on them, not an injustice and not Israelite land greed. Because their wickedness reached its fullness, exactly as God said it would, and He waited four hundred years before He acted. The context begins in Genesis 15. God promises Abraham that his descendants will inherit the land of Canaan, and then He tells him something strange: not yet. Not for four hundred years. And He gives the reason: "the iniquity of the Amorites is not yet full" (Genesis 15:16). The Amorites were the chief tribe among the Canaanites, and the Jebusites and the Hivites and all the rest of them were Canaanites too. So what God is saying to Abraham is this: these people are not yet wicked enough for Me to destroy them, and I will not destroy a people before they have earned it. Your descendants will wait in Egypt until that day comes. That single verse answers most of the objection. God does not act on a whim, and He does not act early. He tolerates sin up to a point, and then He comes and destroys. We saw the same pattern at Sodom and Gomorrah. Abraham bargains Him down: will you spare the city for fifty righteous men? For forty? For thirty? For twenty? For ten? And God says yes every time. He was not looking for a reason to destroy Sodom. He was looking for a reason not to. That is how God works. He is watching every individual, working all day long with His grace, giving people the time and the information and the movements of the Spirit they need to repent, and doing it in respect of their free will. He does not move to destroy until the preponderance of a population is in a state from which there is no return and no hope. Read Hosea on Ephraim if you want to see what this costs Him: God pleading with His own people, saying in effect, please, come back, stop me from having to destroy you. He did the same with Israel, and in the end He had to destroy them too. So when the Canaanites are wiped out, it is not because God was indifferent to them. It is because four centuries of divine patience ran out. There is an older layer to this as well. Go back to Genesis 9 and Noah's curse. The curse falls not on Ham but on Canaan, Noah's grandson, and to my mind that is because Canaan is the one who committed the sin against Noah; it makes no sense for Noah to curse Canaan for something Ham did. Now trace it forward. From Canaan's sin to the conquest you can count the generations, and what you find is that the curse pronounced on Canaan in Genesis 9 is executed in the book of Joshua, when the Canaanites are totally wiped out along with the Jebusites and the Hivites and all the other tribes. That is the finality of the prophecy. So the conquest is not an isolated act of violence. It is the end of a story God announced at the beginning. Two things need to be said to prevent the wrong conclusions. The first is that Israel did not get the land because Israel deserved it. Moses tells them so to their faces in Deuteronomy 9: God's promise to Abraham is irrevocable and you are going in, but do not imagine you are going in because you deserve it, you are a pack of idol worshipers, and in fact every one of you over twenty is going to die in this desert except Joshua and Caleb. God judged the Canaanites for their sin and then judged Israel for hers. That is not favoritism; it is a standard applied consistently. The second is that the commands must be taken as they stand. There is a fashion now, even among Catholic apologists, for saying that God never really commanded these things, that the Israelites made it up and attributed it to Him, or that the language is hyperbole. I reject that, and I have said so publicly to Jimmy Akin and others who take that line. Once you decide the inspired text is lying to you about who gave the order, you have not defended God's goodness, you have destroyed the inerrancy of Scripture to protect a modern sensibility. The text says God commanded it. God has the right to command it, because He is the author of life and the judge of nations, and He had given these nations four hundred years. The lesson here is not that God is arbitrary. The lesson is that God is patient far longer than we would be, and then He is not. The same God who waited four hundred years for the Amorites is waiting on our own culture right now. Do not mistake the waiting for indifference.