The justice and love of God can be described as a paradox. Though not always understandable by finite minds, God is both a God of supreme mercy and supreme justice. His justice demands punishment for sin. However, Eugene Merrill brings up a good point, “Such war was conceived by God, commanded by him, executed by him, and brought by him alone to successful conclusion,” and thus this war was a “holy war.” It was not a war instituted by Moses, Joshua, or the Israelites.
Furthermore, Merrill points out “these apparently mutually exclusive traits (referring to God’s justice and mercy) coexist in the record without resolution. Thus, the moral and ethical dilemma of Yahweh war must also remain without satisfying rational explanation.” In essence, Merrill concludes that since God is good, then everything God commands must also be good.
The apostle Paul expounds on the justice of God in Romans 9:14–18:
What shall we say then? Is there injustice on God’s part? By no means! For he says to Moses, “I will have mercy on whom I have mercy, and I will have compassion on whom I have compassion.” So then it depends not on human will or exertion, but on God, who has mercy. For the Scripture says to Pharaoh, “For this very purpose I have raised you up, that I might show my power in you, and that my name might be proclaimed in all the earth.” So then he has mercy on whomever he wills, and he hardens whomever he wills.
It is God’s prerogative to show mercy on whoever he desires. No one deserves the mercy of God, but he is free to give it to whom he pleases. It was not unjust for God to destroy the Canaanite nations. So, perhaps what might be a better question is “Why has God chosen to show mercy to anyone?”
Yet, while it is certainly true that God ultimately decides what is just and unjust, I hesitate to point only to thie viewpoint when discussing things like the Canaanite Genocide.
For one thing, some have improperly used this to justify unspeakable violence against others today. For another, it has the tendency to come across to modern ears as uncaring and perhaps even an incomplete answer. Will we ever totally understand God? No, of course not, but that doesn’t mean that we don’t try to look deeper into an issue.
 C.S. Cowles, Eugene H. Merrill, Daniel L. Gard, and Tremper Longman III, Show Them No Mercy: 4 Views on God and Canaanite Genocide, (Grand Rapids: Zondervan, 2003), 81.
 Ibid, 94.