I find statements like these aren't honest. Rather than seeking an answer to help them understand and therefore believe, many sceptics use it as a weapon to discourage understanding and belief. They also presume that God is incompetent or not completely sovereign.
One of the reasons I know the Bible is the truth is because it would have been easier to leave this story and others like it out of the Bible. But in order to prove to us that God is indeed completely sovereign, just, merciful and competent, this story and others like it were left in. God wants us to understand Him and if we don't, He wants us to ask Him for the answers. He isn't hiding anything.
The Bible most definitely
DOES NOT teach terrorism and killing of infants. That is very false and and goes completely against God's character. There is a misconception that God does not kill. He does and the Bible clearly shows us (as you've shown with the Amalekites and more) that God kills. However, He does not murder.
First of all the sixth commandment should really say
“Thou shalt not murder.” The Hebrew word for
“kill” used in the commandment,
“raw-tsakh”, has a deeper meaning than just
“to kill.” It applies to murder. It means to kill unlawfully and with wicked intent. Jesus quoted it in this way in
Matthew 19:18, “You shall not murder.” God never murders. In fact
Revelation 22:15 says that murderers will be cast into the lake of fire! The law does not forbid killing in lawful war, or in our defence where necessary etc.
Secondly, only God has the right to take life. He gives us all life. He sustains our lives moment by moment. So He is well within His rights to stop sustaining our lives at any time He chooses.
But when God kills, He does it for a reason whether we understand the reasons or not. It is always merciful and justified though it may not seem so. In the case of the the Amalekites, they were a source of constant torment to Israel. Shortly after the Israelites left Egypt, the Amalekites attacked the weary people, slaughtering the weak and elderly (
Deuteronomy 25:17-19).
The Israelites later avenged the attack and defeated the Amalekites, but failed to completely destroy them. Israel was then plagued with continuous Amalekite raids (
Exodus 17:8-16; Samuel 15:2; Numbers 14:45). God destroyed them to protect His people. He knew Amalekite decedents would always hate His people and try to destroy them. Even today, the name Amalek is a symbol for hatred against Jews. The Amalekites were pagan and had child burning rituals, torture as public entertainment, and sexual immorality as sport.
However God does not just kill people. They always have a chance to repent and change their ways as the story of the Ninevites proves. God warned them through the prophet Jonah to change their ways or be utterly destroyed, and they repented and they weren't destroyed (
Jonah 3). The Amalekites must have had many chances but did not repent and instead would have continued their hatred, murder and destruction against the Israelites and taught their children and grand children the same had God not destroyed them.
Also, had God not destroyed the Amalekites, this world would be in a much worse state than it is in now considering how bad a state its in already. Sometimes God had to nip entire nations to the third and fourth generations in the bud, to save the rest of us (the flood is another example) because He is just and merciful, He is love and knows the beginning from the end. He knows better than us. The Bible tells us 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.
I will add that God saved those innocent children from sinning had they lived and become adults. All children that died before the age of accountability will be saved and will be in heaven and the New earth. Isaiah tells us there will be children in the New earth (
Isaiah 65:17-25). So there are children in the resurrection who obviously must have died while they were children.