Was God just in ordering Joshua to destroy the Canaanites?
Yes, God was perfectly fair and just in commanding Joshua to destroy the Canaanites. Their iniquity had become full, they had gone deep into sin and wickedness, and God had patiently waited while Israel suffered in Egypt so that the Amorites and Canaanites could prove the worthiness of the judgment coming upon them.
Les explains that God was perfectly fair in telling Joshua to kill all the Canaanites, not sparing even an infant or an old person. The reason goes back to Genesis 15, where Israel would have to stay in bondage until the Canaanites' iniquity was full. They had gone so deep into sin and wickedness that God patiently let His own people suffer in Egypt so the Amorites and Canaanites could prove the worthiness of the judgment coming upon them. If any were spared, they would be like a rotten apple in a barrel and cause the rest to go bad. The pitiful part is that Israel did not carry it out, and just as God said, if you do not cleanse the land of them, you will go down to their level, and they did.