God said when you make war you utterly obliterate your enemies, it doesn't matter if they are 20 years old and holding a sword, or two days old and sitting by their mother's side.
If you think your own humanistic morality can trump God's laws, then you are a sad individual indeed.
God doesn't exist to cater to your desires or your so-called morality. He is the absolute sovereign of the universe and His commands are Law. If you don't like it, take it up with Him.
Example... If the nation of Denmark were to declare war on us, the proper response would be to attempt to resolve the matter diplomatically, but if they won't listen to reason and hearken to the words of God, then we embark on a campaign that doesn't end until all the men are dead and the women are taken and distributed to the warriors who fought the best. You level everything and burn it all to the ground.
That's how war is fought, your Geneva conventions and Hague conventions don't mean anything, that's just trying to make something that should be avoided, more tolerable and thus more easily gotten into. War should be kept nasty so people are more hesitant about getting into it. It's not a game or a John Wayne movie, war is nasty, deal with it. That said, I don't think there is any prohibition against showing mercy to conquered enemies as long as they are Godly brethren and it was an issue of some trivial misunderstanding. All too often there were horrible wars in the days of antiquity, one was so bad that Benjamin was nearly wiped out because they stuck up for an Edomite who happened to be living in their land even though he was not a Benjaminite. If Benjamin gets into a war with Judah and Judah wins, Judah is not only not obligated to wipe out Benjamin, they are admonished to show mercy and bring about a fair peace. If you're fighting say, the Hittites or the Canaanites, all bets are off and there is an explicit commandment to wipe them out, man, woman, child, etc... Remember, the Israelites were commanded to utterly destroy the Canaanites, without mercy.
If people from country A were evangelizing paganism or trying to convince God's people away from God, then you go to the nation and kill EVERYBODY and burn the entire thing to the ground, not even taking loot with you lest you wind up contaminated by their decadence and sin. I firmly believe, anybody from some other country, who comes into the USA preaching new-age garbage, witchcraft, or anything other than the word of God, has, by the scripture, doomed the nation that sent them, and has given ample justification for the destruction of their nation. If they want to be left alone they must leave us alone.
