Many struggle with the Old Testament accounts of the wholesale destruction of some nations and cities by God. God destroyed the whole world civilization of Noah's day by a flood (Genesis 6:13) and whole cities by fire, such as Sodom and Gomorrah (Genesis 19). In other cases, He ordered the destruction of Canaanite cities by the armies of Israel (Deuteronomy 7:1-2).
It is important to remember that, while God is a God of love, He is also a holy God, separate from sinners and perfect in righteousness, justice, and purity. The powerful seraphim are pictured as flying and calling, "Holy, holy, holy is the Lord Almighty" (Isaiah 6:3). Judgment against rebellious and indifferent sinners is inevitable, apart from repentance, "for the wages of sin is death" (Romans 6:23a).
God had endured the idolatry, child sacrifice, and moral corruption of the original inhabitants of the land of Canaan for centuries. When He gave the land to Israel and ordered the destruction of the Canaanites it was both judgment on a people hardened against God and protection for Israel lest they be drawn into the corrupt life of the land's inhabitants.
Our difficulty with these acts of judgment is closely associated with our failure to comprehend the purity of God and the sinfulness of mankind, including ourselves. According to the Bible, we all deserve not only physical death but eternal punishment—apart from the death of Jesus as our substitute. Our only hope for escaping the wrath of God is through repentance from sin and by faith in Jesus Christ as our personal Savior and Lord.
In the words of Jesus, "Unless you repent, you too will all perish" (Luke 13:5)—stern words from a God who is "patient with you, not wanting anyone to perish, but everyone to come to repentance." (2 Peter 3:9).
Many people decide that the seemingly senseless acts of God's judgment are a valid reason to reject Him. But this is a serious error. Because God is just, He cannot excuse sin or act somehow as if it did not exist. But because God is also loving, He does not want us to have to endure the punishment we deserve for our sins. We do ourselves no good by thinking we have a greater sense of justice than God Himself.
We must surrender to this truth: "The wages of sin is death, but the gift of God is eternal life in Jesus Christ our Lord" (Romans 6:23). You cannot save yourself from God's judgment—but Christ can, and He will as you commit your life to Him by faith.