I didn't want to get off the trail with the alignment discussion, which seems to be pretty lively atm.
I think to not give the companions alignment tags is not a bad thing. Let their actions speak for them.
I think the problem with just letting their actions speak for them is that there are gods watching the humans and trying to influence what they do. So use a phrase that I often hear against alignment (not from you) "why do you need labels"? "why put things into boxes"?
For me the answer to that goes back to the gods. Different gods control different aspects of the morality and want you act in a certain way. Shadowheart's story is interesting to me because her head and her heart are at odds. For a Sharran, the slaughter of the grove is good thing. One step closer to ending all life and bringing about eternal night.
Likewise Minthara likely worships a lawful evil deity (authority . . . Obey the drow . . . Obey Dror Ragzlin . . ) and so her decision to spare your life puts her at odds with deity.
Playing a cleric or paladin become less interesting when alignment is out of the picture.
And yeah, I'm like you. Had to youtube it. No way I'm going to play "slaughter the innocents"