In the case of Amalek, they were all killed including their children who were not part of the army that attacked Israel, so how do we reconcile that?
Let’s read 1 Samuel 15:1-3, “Samuel also said to Saul, ‘The LORD sent me to anoint you king over His people, over Israel. Now therefore, heed the voice of the words of the LORD. Thus says the LORD of host: I will punish Amalek FOR WHAT THEY DID TO ISRAEL, how he ambushed him on the way when he came up from Egypt. Now go and attack Amalek, and UTTERLY DESTROY ALL THAT THEY HAVE, and do not spare them. But kill both man and woman, INFANT AND NURSING CHILD, ox and sheep, camel and donkey.’” Why would God order the extermination of a whole nation, including infants and children? We see in this passage that Amalek had ambushed Israel many years before this with a desire to EXTERMINATE ISRAEL, including infants and children. Because of Amalek’s desire to “utterly destroy Israel,” God told Moses that He would “utterly destroy them.” We see this in the following two passages:
“Now Amalek came and fought with Israel in Rephidim…Then the LORD said to Moses, ‘Write this for a memorial in the book and recount it in the hearing of Joshua, that I WILL UTTERLY BLOT OUT THE REMEMBRANCE OF AMALEK UNDER HEAVEN.” (Exodus 17:8 & 14).
“Remember what Amalek did to you on the way as you were coming out of Egypt, how he met you on the way and attacked your rear ranks, all the stragglers at your rear, when you were tired and weary; and he did not fear God. Therefore, it shall be, when the LORD your God has given you rest from your enemies all around, in the land which the LORD your God is giving you to possess as an inheritance, that you will BLOT OUT THE REMEMBRANCE OF AMALEK FROM UNDER HEAVEN, YOU SHALL NOT FORGET” (Deuteronomy 25:17-19).
The first passage took place shortly after Israel left Egypt; the second passage was just before Israel entered into the Promised Land (some 40 years after they left Egypt). Israel was “not to forget” what Amalek had done to them, for their vicious attack showed no mercy to “stragglers” and those who were “tired and weary” (these surely included women and young children). If we were to follow the history of Amalek, we would see they were a nomadic people that hated Israel and were known as savages. God knew that they would never change. They would continue to hate Israel and would seek to “utterly destroy them.” Because of their wicked and barbaric behavior, God decided to “blot out the remembrance of the whole nation.” God is HOLY and His decision to judge Amalek was RIGHTEOUS.
Regarding infants and children, God knew they would grow up and become savages (like their parents) who had no conscience in killing innocent people, including women and children. In having them killed, God was showing “MERCY to them” for Scripture teaches us that “all INFANTS who die go to heaven because Christ died on the cross for them” (see Matthew 18:10-14 and then 2 Samuel 12:23). Let’s also remember that though we speak of infants and children as “innocent,” they were still born “in sin” (see Psalm 51:5) and they quickly begin “sinning,” for that is the nature of all humans (Psalm 58:3). (DO) (742.5)