One of the more troubling aspects of the Bible is when God commands or approves the killing of individual people groups. How could God do such a thing? There are many factors to consider when God makes such commands.
Before getting to explanations, what exactly are we talking about? Consider 1 Samuel 15:3, "Now go, attack the Amalekites and totally destroy everything that belongs to them. Do not spare them; put to death men and women, children and infants, cattle and sheep, camels and donkeys.' " Numbers 31:7 states, "They fought against Midian, as the LORD commanded Moses, and killed every man." Again, we see in Numbers 21:3, "The LORD listened to Israel's plea and gave the Canaanites over to them. They completely destroyed them and their towns." Three passages in which God either commands or approves the destruction of entire people groups.
Before addressing the reasons for such commands, it must be understood that all three passages in no way disprove the existence of God. Individuals may not like the passages, but these verses cannot be used to say that God does not exist.
Three good reasons exist to show that it is within reason to justify the punishment of these people groups. The first reason deals with the nature of God. God is described as being a holy God who cannot tolerate sin. These people groups were completely vile and depraved. They were so vile that the sacrifice of their own children was a practice that was engaged in. Not only were they blood thirsty, but they were sexually depraved as well. In reality, no one is innocent in God's eye's and all deserve to be eternally separated from God. All of these people groups could have repented of their sinful lifestyle, but they were content in their evil ways. God foreknew they would never change and therefore called for their destruction.
A second reason for the destruction of these groups is found also in God's nature. God is completely and totally just. In fact, it would have been unjust for these people groups to live and infect the world with their evil practices. This is exactly what did happen to God's own people - the Israelite, after taking possession of the promised land. Because these evil people groups were not exterminated, they brought the Israelites down morally and ultimately led to events whereby the Israelites fell captive to the Babylonian empire. By God allowing evil to go unchecked, would make Him not only unjust, but unworthy of worship.
The third and final reason, deals with the sovereignty of God. The sovereignty of God speaks of his power and authority. If God exist, He and He alone has the ability to rule. God rules with justice and love. He loves all people, but cannot tolerate sin, especially the unchecked sin that existed in the groups God commanded to kill. 2 Peter 3:9 states, "The Lord is not slow in keeping his promise, as some understand slowness. He is patient with you, not wanting anyone to perish, but everyone to come to repentance." God's love today is offered in the sacrifice of His son Jesus. Those who accept Christ will be saved, but those who do not will suffer in being eternally separated from God. If God exists, the created has no right to say to the Creator what He can do. God is completely justified in his command and approval in removing people groups of the past.
- A good article from an acquaintance at Biola dealing with the same subject manner.