We know dualism exists in Tamriel. The Soul is distinct from the Body. Necromancy predominantly focuses on the body, the animation and control of the corpse. And, frankly, i don't see a problem with that. It's a corpse, not a person. If anything, the shadiest ethical side of standard Necromancy is the abuse of Daedra, shoving them into rotting meat-suits and playing them like puppets.
When you start getting into Soul Trapping and such, you start to get into some shadier territory. But i don't think that's really an issue specific to Necromancy. Any sort of conventional Enchanting deals with that.