So I cited RambaM in Hilkhot Melakhim 6:1, who, in turn citing Devarim 20:10, says you cannot wage even a milhemet mitzvah (obligatory war) on the seven nations and `Amaleq until you first proclaim peace. So I said to this fellow that in his effort to obey G-d and listen to G-d rather than his conscience - an admirable goal, to be sure - he'd actually have become a murderer according to the Torah.
The Yerushalmi tells us that Joshua sent three letters to the Canaanites, one offering them to accept the Noahide laws and live with us in peace, one offering them the option of leaving Israel, and the third resorting to a declaration of war if they refused the first two options. Evidently, even with the Canaanites, the option of accepting the Noahide laws and peace always existed. Indeed, is not Rahav a most superb example for us? Despite the fact that her entire society and city rejected peace and chose war, she herself chose the Noahide laws and peace, and Joshua not only accepted her, but even married her! So we see that even specific, individual Canaanites or Amaleqites could choose peace, even if all their neighbors chose otherwise. (The Torah truly does value the individual, after all.)
So back to our case of the nice Amaleqite mother, if my fundamentalist disputant had killed the nice woman and child, and the same man in a second alternate parallel dimension had let her live, thinking, "I don't know how or why to justify my failure to obey G-d's command to kill her, but I'm not killing her anyway, and please G-d, I'll find out how and why later", in that case, when both men would have read RambaM, the first would be mortified and the second gratified. In turns out that the second man, who held onto his reason and refused to obey what was ostensibly G-d's command, actually turned out to obey G-d more than the man who defenestrated his reason and conscience and attempted to obey G-d.
Of course, where Avraham acquiesces to G-d at the Aqeida (binding of Yitzhak for sacrifice) is a puzzle, since Avraham at Sodom had confronted G-d and asked "Will not the judge of all the earth do justly?". Rabbi Dr. Isidore Epstein in The Faith of Judaism has an interesting answer. He says that with the Aqeidah, the Torah uses the name Eloqim, whereas with Sodom and `Amorah, it uses Hashem. Rabbi Epstein uses the Kuzari-ian distinction between the far-away G-d of the philosophers and nature versus the intimate G-d of love and personality to explain why Avraham felt justified in arguing in one case and not the other. And of course, Avraham knew this was G-d talking to him, whereas the Torah doesn't inspire quite the same sense of immanence and immediacyin us, and I believe we are more justified in taking a shev v'al ta'aseh ("sit and do nothing") attitude when it doesn't comport with us, whereas Avraham could not make this excuse that G-d's command was not so immediate and striking.
The Midrash says that this was Avraham Avinu's hardest test because he had been preaching to everyone that human sacrifice is evil, and that now, he was to become a hypocrite and contradict everything he had already taught the heathens. According to the Midrash, it seems, Avraham did know that human sacrifice is wrong, and so the only reason he was willing to go through with the Aqeida was that G-d said so, and he knew that G-d had said so. The ethical dilemma for Avraham was just as clear to him as it is to us today - if not even clearer for him than for us - according to the Midrash.
Anyway, the way I figure it, here's what I'll do if someday I receive a prophecy from G-d to do something violent. The dialogue will go something like this, I figure:
G-d, could You please explain to me why I'm supposed to do this, and how it is justifiable, and how it doesn't contradict what else You've taught me? No, no, no, it's NOT that I'll only obey You if You can give me a good reason - of course not! It's just that if I obey You right now - which I surely will, of course - I won't understand why in the future I shouldn't continue to do violence. I mean, You've told me not to murder, etc., and now You're telling me to murder. Sure, I'll obey You now, but if I do so, I'll lose my ethical sense, and I won't understand why in the future I shouldn't murder anymore. G-d, RambaM tells me in Shemonah Peraqim that I shouldn't even desire to do a transgression of a mitzvah bein adam l'havero (interpersonal social mitzvah), that my own inner desire should eventually become one that conforms to Yours, without my having to consciously tell myself, 'I'd like to sin, but G-d forbids it.' (By contrast, of course, with a mitzvah bein adam la-maqom (a ritual mitzvah), I am to tell myself nothing other than that I'd love to do it were it not for G-d's command; I am to love pork and desist only because G-d says so.) But if I obey Your seemingly unjust command - which I certainly will obey You, of course! - then I will lose this inner ethical sense in my conscience, and I won't be able to obey You as well in the future anymore. So please G-d, tell me why I am to do this act of apparent injustice now, so that I understand why this doesn't contradict the general prohibition of injustice to which I will ordinarily be bound. I'll obey You now regardless of what You say, but I'm afraid that unless You tell me why I am to commit an act of injustice, that I'll continue to commit acts of injustice in the future.
Furthermore, G-d, the Torah teaches us that on one occasion, Avraham asked you, "Shall not the Judge of the earth do justly?", and yet on the other occasion, he acquiesced to You without question. Look, G-d, I cannot read Avraham's mind and know why he did what, and I certainly do not profess to have a perfect understanding of the Torah. So I'm not sure which example of Avraham's I am to follow. Now, You have commanded me to violate one of Your mitzvot, and safeq d'oraita l'humra ("in a case of doubt regarding a Torah mitzvah, take the more stringent option"), so if anything, I should be mahmir (strict) and follow the shev v'al ta'aseh ("sit and do nothing") approach and question you as Avraham did at Sodom, and not acquiesce as he did for the Aqeida. Look, G-d, I'm not a genius, so what do I know except to follow the examples You've recorded for me in Your Torah? I'm just trying to follow what You gave me.