The "ban" refers to God telling the Israelites that when they enter into Canaan they need to kill everything, men, women, and children. That, no doubt about it, seems harsh and cruel. My goal is not to explain that away in this post, or to explain it at all, really, but rather to give one example of why that might have been necessary.
In Numbers 31 Israel defeats the nation of Midian. As spoils of war, the army takes typical treasure: loot, livestock, and women (and before we get all high and mighty about how much we've changed in the modern era, the spoils of war are still the same: trinkets, economic treasure, and sex). When the army returns to camp, Moses meets them, not proud of their accomplishment in battle, but angry of the women they've captured. These women are the very same women who seduced the Israelite men into worshiping Baal a few chapter back. In fact, they were bait Balaam used to derail the Israelites when God wouldn't let Balaam curse them. These women would be a cancerous presence in the nation of Israel. They would keep Israel from fulfilling the purpose God had brought them out of Egypt to accomplish. What's really sad about all this is the fact that the Israelite warriors didn't seem to remember this at all. In typical male fashion, their higher intellect seemed to stall out at, "Ooh, pretty."
Now does this make the ban sound any more palatable to us? Absolutely not, but it does bring light to the fact that there are bigger issues going on then Group A wants to live where Group B is, so Group A is justified in genocide. This is not Hutu vs. Tutsi, Bronze Age version. This is "Does Humanity Have a Future" Bronze Age version.
Stopping Point: Numbers 32