Not to add to the the misunderstood villain fuel, since I hate that, but an EQD thing just think of a:
Crazy theory
With this wonderful screencap
here, we know the door trap makes Twilight's eyes go glowy green and red, a la dark magic. What if Sombra got trapped by the door (made by someone else even further back), and then, afraid of his worse fear, made sure it would never come to pass (by enslaving the crystal ponies). That is why his eyes are as they are, not because of the dark magic (which came later). Then he gets smoked (hah!) and actually goes insane.
Using an Occam's razor approach, this makes no sense, and I personally don't like it either, but I figured I'd throw it out there for people to chew on.