To me the soul gem concept is a plot hole in the TES lore since it is never touched upon as an immoral thing.
It's no more immoral than raising and harvesting chickens/ducks/cattle, or hunting deer.
Unless we're using Black Souls here.
You can go assassinate NPCs for the Dark Brotherhood; and when necessary for other guilds. The deadra gods have some real gruesome quests that go way beyond assassinations - you have to lure innocent people to their deaths. You have to kill defenseless animals for their hides so you can level smithing. How about killing Falmer - what have they done to you?
But none of that bothers you - but putting a soul inside a gem does.
It's a game people, not real life.
I can't bring myself to do any of that. Those I've killed for Daedra were either against my will (The Vigilant of Stendarr for Molag Baal - We were trapped and he went crazy), and I've walked away from all others. The Dark Brotherhood is dead in my game, killed by my blade. A shame the guards had a cold that day.
As for the Falmer - Have you
seen what they've done to those who wish to travel between Whiterun and Solitude?