To be honest I think the lack of human enemies is Nintendo's way of showing a world where good and evil are definately defined and are immediately recognizable. It's refreshing to be able to see a creature and easily being able to say "that's evil".
But maybe I'm overthinking things.
Anyway, I think that for Link to kill humans in a 3D game the story would have to be appropriate and the deaths should be seen as necessary.
EDIT:Wait, I just realized. Doesn't Link kill soldiers in
ALttP?