Sof Davar, many peole believe the history in the Torah and dismiss any reference to Hashem and Nevua. You’d have to fight that issue first. The common attitude is to lump everything into one pot: Amalek, Islam killings, Crusades and Inquisition. To us, the main difference is between truth and falseness, but to those who don’t believe it has to be explained.
It is important to make the distinction clear. Amalek was always our enemy, and a barbaric on at that. Take a look at what Shmuel told Agag.
We are not merely saying that anything immoral becomes moral if Hashem tells you to do it. On the contrary, Hit can’t be that Hashem will command something immoral. We are saying that in the justified war against Amalek, who was always our bitter enemy, we were told by the One who knows them best not to leave anyone alive.