But thou shalt utterly destroy them; namely, the Hittites, and the Amorites, the Canaanites, and the Perizzites, the Hivites, and the Jebusites; as the Lord thy God hath commanded thee: (emphasis added)
I don't know about you guys, but that's a lot of -ites that are required to be destroyed by one group of people. The Lord doesn't just say who has to be destroyed, but how the Israelites are supposed to treat these people. This information can be found in Deuteronomy 2:15, 7:2, and 12:2-3, and the picture is pretty dark.
We have seen plenty of movies where the bad-guys come through and just be evil bad guys. They burn down houses, churches, destroy a land with no mercy or second though as to who they're hurting - that's always the bad-guys job. But the Lord tells the Israelites to do this to all the other -ites listed above - to show no mercy, to destroy everything, particularly their altars and images to false gods. At least at this point we understand why God wants the people destroyed - they have forgotten Him and turned to false gods, so He is angry, and has asked His faithful people to work for Him in His name.
In Deuteronomy 9:4-5 and page 219 of the Institute Manual, it is explained that idolatry was not the only reason that the Israelites were commanded to kill the Canaanites. The Canaanites were ripe in iniquity, practicing prostitution and homosexuality as religion, completely rejecting the word of God and they were proud of it. Because of this, God sanctioned them to death, because to show them any kind of mercy would have led the Israelites astray. How the Israelites treated the Canaanites became their own judgement.
Obviously, we can find these same sins in today's society. They are becoming commonplace so it is harder and harder to just keep away or ignore these sins. It is important that we take our stand with God and always stay by Him no matter what other people may say. We must make our beliefs clear, and make it even clearer that we will not make any exceptions. By making not exceptions, by showing no mercy in this way, we can act like we should in the name of God to help keep ourselves clean.