Killing children is never just. Is the killing of the babe instead of the mother in a dangerous pregnancy just. Did the child receive its just reward for simply trying to be born? Nevertheless, a difficult decision had to be made, and the mother was saved alive. Justice for the children is not the concern in 1Samuel 15. Nevertheless, a difficult decision was made, and that according to the preferred choice in the ANE culture. Most cultures preferred a quick death over a slow, painful one. Moreover, historical records of any age show us that most cultures also preferred death to slavery.
Moreover, we need to consider the responsibility of the end of the matter. Why did Saul attack Amalek in 1Samuel 15? It was because Amalek was unmerciful in its relationship with Israel. First they attacked the weary and feeble as they left Egypt and a distance separated them from the main body of the nation (cf. 1Samuel 15:2). Secondly, Saul attacked Amalek because over a period of 400 years the Amalekites had been plundering southern Israel, destroying crops and enslaving Jewish women and children (cf. 1Saumel 14:48). Over the centuries tens of thousands of Jewish families were affected, perhaps numbering into the hundreds of thousands individually. Clearly something had to be done. Certainly, it cannot be expected that Israel take no action against her enemies, and war is not a glorious story about how the hero was victorious over his enemies, without ever hurting the innocent. What war is ever like that?
If Amalek behaved differently and didn’t plunder its neighbors, his women and children would have been safe. We need to lay the responsibility of the deaths of the women and children in the proper place. The responsibility of the death of the wicked does not lay with the executioner, but his blood is upon his own head (cf. Joshua 2:19; 2Samuel 1:16).
“But…” the Biblical critic exclaims, how does the killing of children amount to justice? It doesn’t. Killing Amalek’s children was never the intent of Saul’s campaign, anymore than the killing of Amalek’s livestock was the intent of the war (1Samuel 15:3). The responsibility of the safety of Amalekite families lay in the hands of the Amalekite warriors who terrorized southern Israel. Saul set out to punish those who had plundered his nation and abused his people, namely, Amalek’s warrior class. Moreover, God’s command to kill the livestock was to show the war was not meant to profit Israel, but was meant to carry out justice against a prodigiously violent enemy who never ceased to wage its terror upon the inhabitants of southern Israel.
“But…” the Biblical critic exclaims, if God is truly omnipotent couldn’t he have done something else to save the innocent? The problem with this argument is that the Bible rarely shows God omnipotently acting in history. Generally, the Bible shows God works within the affairs of men, not infringing upon our free will. In so doing God brings his will to pass (cf. Daniel 4:35), while men seek to realize their own goals. In showing his omnipotent power by judging Egypt, the other nations, including Amalek, should have been afraid to attack Israel, but they weren’t. Moreover, God expressed his patience with Amalek for about 400 years in an effort for the nation to come to its senses and cease its terroristic tendencies. It did not. While some Amalekites did migrate elsewhere, including to Israel (2Samuel 1:13) where they were accepted (!), the main body never ceased its plundering Israel. Why wouldn’t God judge them? Why wouldn’t Israel wage war upon them?
The point is that we live in a real world and must live with the consequences of our decisions. God, normally, doesn’t infringe upon the cause and effect rule in our daily lives. Amalek plundered southern Israel for about four centuries before Israel was able to retaliate. Amalek destroyed crops, killed fathers and husbands, and enslaved wives, mothers and children. Who should be held responsible for the deaths of the Amalekite children—Israel or Amalek? Amalek was the aggressor; Israel rose up only to retaliate and cause Amalek to cease its terrorist activity. God works out his will for us in the real world. He works with us, not upon us. He seeks to help us improve our behavior without destroying our culture. He will even work within bad situations, such as war, slavery and flawed social conditions, in order to bring about a better result. He is not responsible for the wickedness of men or for the fruit of that wickedness. Men are responsible for their own behavior and for whatever events transpire as a result of that behavior.
 He does at creation and again to judge the world with the Flood in the time of Noah. He confused the languages in Genesis 11, and judged Sodom and the cities in the plane in Genesis 19, and he judged Egypt in order to free Israel.