You're either trolling or seriously deluded. Sanctuary's humans are a direct analogue to reality's humans. If killing a baby (or a million of them) because it "could be evil later" is a good thing in Sanctuary, then it's a good thing in reality. If it's not a good thing in reality, then it's not a good thing in Sanctuary. If it's good for them to kill innocents based on perceived evildoing with no objective justification for the perception, then the same thing applies to the Nephalem.

There is no objective justification (because nobody ever met Anu and therefore nobody can accurately claim that he–or more importantly, his spawn–is actually omnibenevolent), therefore the Nephalem has the same basis for murder as the angels do. Malthael was about to kill a bunch of people for no good reason, so you're justified to retaliate. You're just as moral as he is. Actually a lot more so, since you're not holding all angels accountable for the misdeeds of one, because your character isn't a total shitlord.