I don’t deal easily with it. It’s hard. Any parent doesn’t deal easily with a command to kill children. In light of the sermon on the age of accountability, I believe those children are not yet accountable for their sins, and though God commanded Israel to completely destroy Canaan, the children are with him in heaven.
God’s concern about Canaan and other nations surrounding Israel was connected to his commands to Israel in Exodus 34:15-16, “lest you make a covenant with the inhabitants of the land, and they play the harlot with their gods and make sacrifice to their gods, and one of them invites you and you eat of his sacrifice, and you take of his daughters for your sons, and his daughters play the harlot with their gods and make your sons play the harlot with their gods.” Israel was always, as we are, tempted to leave God and pursue other gods. If they did not completely eradicate pagan nations, they would eventually pursue those gods. As a matter of fact, Israel eventually followed the ways of Canaan, even sacrificing their own children to the God Molech.
Completely eradicating Canaan served to protect Israel from them and to protect Canaan from themselves. While this will always be difficult to understand, it must serve as a staunch reminder of the danger of sin and of how seriously God takes sin, especially the sin of idolatry.