Genocide in the Bible?

Why did God instruct Moses and the Israelites to wipe out entire communities when they entered the promised land?

Short answer: Nagasaki and Dresden.

Longer answer: 1. Why did we kill a quarter million in Nagasaki and over a million in the fire bombings of Dresden? Because we were fighting against unjust states and unjust states cannot exist without popular support; because the people, through their leaders, committed unjust actions. E.g. Germany acted as an aggressor against Poland and perpetrated genocide against the Jews; likewise Japan tried to conquer other territory and they committed great slaughter and other unmentionable outrages against the Chinese). For these acts they both deserved punishment and our bombs did the punishing.

The ancient occupying societies of Israel were about as unjust as societies can be. Child sacrifice was rampant and of those that lived, the majority (if not all), of the kids were at an early age forced to work as cultic prostitutes. The people in these societies either actively participated in these despicable acts or they were complacent. Therefore all of them deserved death.

2. Going along with this, ancient societies had more of a collective notion of guilt, rather than a more modern notion of individual guilt. Societies, not just the individuals, were guilty of crimes. Think of Achan from the Book of Joshua Chapter 7. Achan disobeyed God after the military defeat of Jericho by stealing goods reserved for the Lord. As a result of his sin Israel suffers military defeat. All the people suffer until he is punished for sins have collective consequences.

When a society sins it effects the land like a cancer (e.g. Abel's blood cries out from the ground, the Law talks about blood guilt and healing for the land, and the prophets over and over repeat that the land cries out against injustice). So again, when a society lives in rampant injustice they must be wiped out in order to cleanse the land (think of Sodom, and when all the earth was evil, the flood).

3. Finally, the actions of the Israelites were in line with the rules of warfare at that time. If a town surrendered, you treated them well. But if they resisted it was expected that you would wipe them out (for the hardship you endured in besieging them). This is what Rome eventually did to Carthage. At first they showed mercy, but a generation after they had first defeated Carthage, they themselves were almost defeated by Carthage. Annihilation was the only way to be safe. In the same way Israel’s safety, to some degree, required them to completely defeat their enemies. (And oddly enough Carthage was a Phoenician colony that worshiped the same child 'eating' God Baal as did the inhabitants of ancient Israel).

4. One more things must be noted: in the case of Israel, none of these people had to die. There were instructions in the law of how to bring outsiders into the Israelite community (if they so desired). We have examples of this in Rahab and Ruth. Both were so integrated into the Israelite community that from their lines descended Christ, and Ruth herself was the grandmother of King David.

Judgment only befell those who rejected the invitation to join the Israelites (and we have no idea how many people joined or refused to join them). In the same way Noah invited people to join his ark, but those that rejected this invitation incurred judgment. There is an obvious parallel with salvation here. God invites all to join His people. It is only those that reject this invitation that will meet judgment (in their case, Hell).

Paul says that the stories in the OT are examples for us of spiritual truth. Those that rejected the invitation to join God's community were judged by means of temporal/physical death. In the same way those that reject the invitation into the Church will be judged by eternal/spiritual death. The former is like a living parable (just as Isaac was a Christ figure, the Red Sea a form of baptism, etc).