Every time people lament changes to the lore that amount to "not every member of species X is irredeemably evil" and claim the game is removing villains from it, I think how villains of so-caleld evil species fall into two cathegories: a) bland and boring and b)have something else, unrelated to their species going on for them, that makes them interesting.
If you can kill something without feeling bad because of its race, that's fucked up. A group of goblin bandits can be fun, but they're villains because of the bandit thing, not the goblin thing. Why should a group defined by plundering travelers be more acceptable than a group defined by being short with green skin?
That said, the undead are, more often than not, fair game. Undead are a mockery of the life that came before and a defilement of their corpse, so killing them is a way of honouring the dead.