Morals and Halacha

peace!
The question follows the debate with Yaron Yadan and some of your lessons that I heard.
You claimed that the source of morality and law is God.
You said that in certain cases when there is a conflict between morality and halakha, you will prefer halakha over morality. You gave the example of killing the Amalekites. You reasoned that since this is explicit in the Torah, it is a sign that God probably expects you to violate a conscientious command and commit murder.
Following this, a few questions:
1. If I killed an Amalekite, surely because of a divine command, did I do something wrong and should I be judged?
2. Is a Muslim who kills a person an infidel according to his system because of a divine command, assuming that it is explicitly stated in his tradition/holy book that it is from God? Has he committed a bad deed and should he be judged?