In Deuteronomy 25:18 the scripture says Amalek struck out at the most feeble of Israel, those who were tired and straggled behind the main body. Afterward in Exodus 17:1, 8 Amalek attacked Israel while they rested and sought water at Rephidim. Because of these two unprovoked occurrences, God told Moses that he intended to destroy the remembrance of Amalek among the nations (Exodus 17:14) through the efforts of Israel (Deuteronomy 25:19). Amalek was a warring, nomadic nation who survived by raiding peaceful settlements and looting food supplies and anything they could sell for profit. Nevertheless, what can we say about God’s judgment of them, namely to “utterly wipe out the remembrance of Amalek from under heaven” (Exodus 17:14)? Does this amount to genocide?
None of God’s judgments, including this one, could ever be rightly understood as genocide. To begin with, the Scriptures tell us that the Lord will be at war with Amalek from generation to generation (Exodus 17:17), and this war will be fought through Israel (Deuteronomy 25:19). Knowing this, how could we point to a time or a battle that was supposed to completely wipe out the nation of Amalek? Some folks believe that battle (or campaign) was fought by Saul in 1Samuel 15, but this isn’t true. Notice:
1Sa 15:2-3 Thus saith the LORD of hosts, I remember that which Amalek did to Israel, how he laid wait for him in the way, when he came up from Egypt. (3) Now go and smite Amalek, and utterly destroy all that they have, and spare them not; but slay both man and woman, infant and suckling, ox and sheep, camel and ass. (emphasis mine)
This text on the surface does appear incriminating, and no matter what can be decided in the end about responsibility, it is indeed a tragedy that non-combatants, especially women, children and babies suffer and die during war.
Consider for a moment that Saul’s campaign against Amalek took place some 400 years after Israel left Egypt. During those 400 years there is little doubt that Amalek had not ceased its efforts to prey upon the weak and peaceful non-combatants of southern Israel (1Samuel 14:48; cf. Judges 3:13; 6:3-5; 7:1 2; 10:12). No mercy was shown to women, children or the weak in Israel during Amalek’s plundering. On this note, whose responsibility is it when the innocent suffer in war? Does the responsibility lie with the aggressor whose attacks are sudden and unprovoked or is the one who retaliates against this violent and unmerciful enemy, the one who is responsible for the tragedy of war? Such questions require complex replies.
A modern example of such complex issues might be the debate over the atomic bombings of Japan by the U.S. during World War II. Was the U.S. responsible for the Japanese deaths incurred over the Hiroshima and Nagasaki atomic bombings that ended World War II, or did the Japanese bring the deaths upon themselves by their unprovoked attack on Pearl Harbor 2 ½ years earlier? One might accuse the U.S. of indiscriminately killing many non-combatants, including woman, children and babies. Yet, experts judged the deaths incurred in those two cities (cir. 130,000) saved the lives of not only one million to a million and a half of the Allied forces, but probably curtailed the number of Japanese casualties as well, had an invasion of her beaches (scheduled for November 1945) become necessary.
The Scriptures repeatedly show that responsibility for judgment against wrongdoing lay upon the shoulders of the wicked (Joshua 2:19; 2Samuel 1:16; 1Kings 2:32). Even today, if a father is an alcoholic or abuses drugs, his family suffers with him, even if they don’t do the same things he does. The innocent suffer because of the deeds of those in authority, whether that might be the head of a family or the head of the state. There is no easy answer for complex issues like these, and, when one adds warfare to the mix, the pain and injustice become even more terrible. Additionally, the solutions to these problems increase exponentially.
The bottom line is that God never commanded to destroy every Amalekite. Genocide was never an issue. On the contrary, even after Saul’s campaign against the Amalekites, David also had to wage war against them in 1Samuel 27:8-9. Neither did David kill them all at that time, since he had to later fight another band who had taken his wives and children and the families of those with him (1Samuel 30:17-18). Moreover, long after David’s death the Amalekites were still around in the days of Hezekiah, King of Judah (1Chronicles 4:41-43). Therefore, just as God’s judgment against the Canaanites was never meant to be genocide, his judgment against Amalek in Exodus 17:14 and Deuteronomy 25:19 has at least as much to do with simply driving the people out of their land as it does with warfare. The end would be the dispersion of Amalek among the nations (Deuteronomy 32:26). Thus, wiping out their name or national remembrance from under heaven, which is what the Scripture says God intended on doing.
 I’ll speak more directly to the killing of children in another posting when I come to God dealing with the Midianites.