My Apologetics study Bible included an article by Matt Flanagan entitled, “Does The Bible Condone Genocide?” He tells us the ancient writers used “extravagant exaggerations” as was common in literature at the time. Flanagan sites the fact that the Bible reports some of the nations (like Canaan) continued to have citizens even after it tells us they were wiped out. Therefore, the report of the genocide was exaggerated for literatures’ sake.
Which, to me isn’t so much exaggeration as it is disobedience. The Israelites may have wiped out a village or two, but obviously didn’t do a complete job elsewhere. The hard truth is that in Old Testament scripture, God didn’t only condone genocide, He commanded it.
Now, before you get too angry with me, or angry with God, you need to take a look at the whole picture. Here is what seems to be overlooked by some:
When you approach a city to fight against it, make an offer of peace. If it accepts your offer of peace and opens its gates to you, all the people found in it will become forced laborers for you and serve you. However, if it does not make peace with you but wages war against you, lay siege to it. (20:10-12)
Before the Israelites went to war against a city they were to offer a peaceful solution. God wanted those people to come to Him on His terms, and be saved. Their refusal cost them their lives.
There are two things I take away from this today:
- God will not demand nor condone genocide after the cross. Jesus fulfilled all the requirements of the Law, and made it plain our enemy is no longer flesh and blood. His kingdom is spiritual. We must protect His spiritual kingdom by eradicating sin from among us with the same completeness the Old Testament Jews were told to eradicate people who rejected God. We will not be commanded to kill people. We are commanded to destroy sin in our lives.
- The Jewish people had to fight against Canaanites during their entire existence as recorded in the Old Testament. Had they obeyed, and truly dealt with God’s enemies like He told them to, their lives would have looked a lot different. Better. Peaceful. The same goes for us. How much grief do we face when we simply play around with sin, when we hold on to that sinful thought or feeling, when we aren’t exactly honest, or when we tolerate sin even in small doses? The Canaanites didn’t just go away on their own. And neither does sin.
Yes, it’s hard to even think about the genocide God ordered in the Old Testament. But these were not innocent people. They were people who would rather die in their sin than accept the peace God offered if they’d only surrendered.
That sin you are holding onto isn’t innocent, either.
alighttomyway 
In the next few verses in Deut. 20, God did command that “you shall let nothing remain alive that breathes, but you shall utterly destroy them: the Hittite and the Amorite and the Canaanite and the Perizzite and the Hivite and the Jebusite, just as the LORD your God commanded you.” The reason for that was to prevent them from teaching Israel “to do according to all their abominations, which they have done for their gods, and you sin against the LORD your God,” vs. 17-18. The Canaanites were not an innocent, childlike people. They were depraved beyond our understanding, even to the burning alive of their infant children in worship of “their gods.” Their extermination was a judgment for their sins, as well as to protect Israel. Israel failed. Israel wound up doing the same things. Israel wound up being judged for their sins. It’s only through the mercy of God and the fact that He has promised them “a future and a hope,” Jeremiah 29:11, that they, too, haven’t been wiped out as a nation.
You are right. They were far from being innocent people. And yet God gave them chance after chance to see Him and surrender to Him before He destroyed them. Oh, that we would recognize how serious God is about sin, and how awful the punishment for unrepentant sinners. I pray that God’s people will rid ourselves of sin in our own lives, and be bold to share the truth of God’s mercy with people who need to hear it.