Personally, I figure if they are big enough to swing a club at my head, they are fair game.

At least inside the mine, you might be able to avoid killing the baby trolls (I think only the large, Runekeeper troll needs to be defeated to progress). You can make peace with Mundus, which will make the trolls in that area friendly; I don't know if it will affect any remaining trolls throughout the rest of the mine.