If the Israelites were to subdue the land and live out the dominion mandate as a kingdom of priests to the rest of the world, holiness or purity of worship was absolutely necessary.
Genesis 15:16 and Leviticus 18:24-25 indicates that placing the Canaanites under the ban was a judicial matter, but the Canaanites were put also under the ban so that Israel would not be adversely affected by the Canaanites (Deut. 7:1-4; 20:17-18). Israel would not be an effective priest to the nations (Ex. 19:6; Deut. 4:5-8) if it succumbed to the sins of the Canaanites.
Thus, ironic as it may sound, the extermination of the Canaanites seems to include a missionary motive.