It is an issue that Christians grapple with and quite frankly often find very uncomfortable - the slaughter of the Canaanites. While the distance in terms of time, space and culture means we are not really well-placed to enter into all the circumstances I want to attempt to address the issue in a concise way here, showing that Scripture gives us enough to go on.
It is clear that the nations occupying the land were guilty of unspeakable wickedness (Leviticus 18 v 24-30; 20 v 23; Deuteronomy 18 v 9-14; 2Kings 16 v 3). Because of this wickedness God was going to wipe them off the face of the earth. It may be asked why God didn't do this directly instead of using Israel. A possible reason is that God might have wanted Israel to do it to teach them graphically the consequences of such sinful behaviour, and He warned them that emulating their behaviour would result in their expulsion from the land too. It has been suggested that the immorality practised by the nations would mean they would be riddled with diseases that demanded their complete wipe out.
However, Scripture tells us that the nations had been given a long period of grace in which they could repent (Genesis 15 v 16). It is also evident that they knew well about the Exodus and what God had done to the Egyptians and for the Israelites (Joshua 2 v 9-14). The miraculous signs evidenced the fact that God was with them, they should then have yielded to the Israelites but instead they fought against them. There was a way of salvation available for them, of which Rahab and her family availed.
The biggest problem people have is that the slaughter was to include children, and there are a couple of things to bear in mind in relation to this issue:
1. The nations were at war with Israel, and when the head of a nation / family (or race, e.g. Adam) acts everyone under his headship is affected.
2. The nation of Israel wasn’t in a position in which they could look after the children of all the nations they were expelling from the land.
3. The children would be in heaven if they were under the age of accountability and thus would suffer no ultimate harm.
4. Life is God’s to take however and whenever He chooses and if He believes it is best for certain people not to live then we are in no position and have no right to argue.
It is at this last point that the atheist would find himself in a bit of a bind because if he allows the possibility of God’s existence then he can’t deny the point, but if he insists God doesn’t exist then he has no right to call anything unjust or immoral because he has removed the foundation for judging such things. The question to ask is, if he says the slaughter of the Canaanites was immoral, “By whose standards?” If he answers that their actions are unjust by his standards then the sharp response would be "So what?" Or you could be more gentle and ask, "Why should your standards be imposed on anyone else?" The objection needs God's existence in order for it to gain any traction, but if God exists then the objection crumbles because God has sovereign rights over His creation and could have morally justifiable reasons that we may not even be able to conceive.
Some people who don’t think these issues through make far more of them than is warranted, for example, they will say that such a thing justifies killing immoral people now. It does no such thing, because the passages that talk about the slaughters are not didactic teachings telling us how we ought to live our lives, but they are narrative passages giving us history. There are no passages in Scripture that teach people to kill others for the spread of the Gospel, and there are clear passages that teach against it. Humans do not have the right to give or take life, only God does, and there are some circumstances in which he has decreed that humans will be His instruments to carry out that action of taking life (e.g. Government executing criminals for capital crime). Due to the completion of the revelation of Scripture we can be sure that anyone claiming God told them to carry out a killing is wrong because God has given His decrees and revealed His will in Scripture.
