[quoted from http://www.amazingfacts.org/Publication ... fault.aspx ]
Why did God order genocide?
Q. Why did God order the genocide of the Amalekites, including women and children?
A. Many people are naturally perplexed by what appears at first glance to be a paradox in God’s actions and character. He commands us to love and forgive one another, even our enemies. And one of the Ten Commandments tells us not to kill (Exodus 20:13). So is what God commanded against the Caananites and Amalekites a contradiction?
First, the sixth commandment word “raw-tsakh,” translated as "kill" in the King James, has a deeper meaning that just “to kill.” According to Strong’s, it applies “especially to murder.” Christ bears this out in Mathew 19:18 when He says, “You shall not murder.” Perhaps Matthew Henry explains it best: “It does not forbid killing in lawful war, or in our own necessary defense, nor the magistrate’s putting offenders to death, for those things tend to the preserving of life.” This explains how David could be a man after God’s own heart and still be honored for his courage in killing Goliath.
Regarding the command to eradicate entire nations, I believe that God had to because the influence of these nations left unchecked would ultimately lead to the death of many more innocent people. It’s helpful to keep in mind that nations like the Canaanites engaged in human sacrifice, even offering their children to devil gods. (See Deuteronomy 12:31.) Additionally, not only did God use Israel’s might to punish evil nations like these, He used the Babylonian, Assyrian, and Egyptian kings to punish Israel. God will often use human forces to mete out His discipline.
It’s an imperfect illustration, but often infected cattle or poultry are destroyed for the purpose of stopping an epidemic and saving vastly more livestock. Likewise, left unchecked, these nations would have plagued the world with such depravity that they simply were not redeemable. So as much as it broke the heart of God, the order was given to eliminate these infected nations.
The Consequences of Failure
The Amalekites were a source of constant woe to Israel. Shortly after the Israelites left Egypt, the Amalekites attacked the weary people, slaughtering the weak and elderly (Deuteronomy 25:18). Even the Babylonians had a bad opinion of them, calling them “Khabbati,” or “plunderers.” The Amalekites and Caananites, among other nations, practiced child burning, torture as public entertainment, and sexual immorality as sport.
The Israelites later avenged the attack and defeated the Amalekites, but failed to completely eradicate the nation. Israel was then plagued with continuous Amalekite raids (Exodus 17; 1 Samuel 15:2; Numbers 14:45). We can safely assume that God knew Amalekite decedents would always bear rage against His people. In the book of Esther, Haman the son of the Agagite, who was an Amalekite king, sought to exterminate all the Jews. Even today, the name Amalek is a symbol for hatred against Jews. How different things might be had Israel obeyed God to the letter?
You should also remember the story of the Ninevites. God was warning them through Jonah to change their ways or be utterly destroyed, and they repented. God deals far more justly and mercifully than most people are willing to admit.
No Easy Answers
This is a very difficult issue. Honestly, I don’t always understand God because I’m not God. But at the same time, I trust God that He is just and that He is love. We serve a sovereign and eternal God who knows better than we do, and though we now look at Him through a glass darkly, one day will come when we will have clear answers. Remember that God’s ways are higher than our ways and His thoughts are higher than our thoughts (Isaiah 55:9; Romans 11:33–36). We have to be willing to trust God and have faith in Him even when we do not understand.
Often, questions like these aren’t honest. Rather than seeking an answer to help them believe, many skeptics use it as a weapon to discourage belief. It is certainly not a new question. It also presumes that God is incompetent or not wholly sovereign. They say, “I wouldn’t do anything like that, so God shouldn’t either.” But the framework of the Bible is that God is indeed sovereign, just, and competent, which is exactly why writers left the story in. God wasn’t hiding, and He’s hoping people come to Him for the answer.
Yet a genuine question deserves a genuine response, and I hope I’ve given you some helpful nuggets of wisdom to answer a truly difficult question. Quite simply, for God’s faithful, it is a matter of trust. Yes, we know that God is good, that He wants the best, but ultimately, we have to trust Him.