He's neutral, that's how I see it. The Daedric princes are beyond notions of good and evil. Though we see what they do as evil, they themselves are amoral, they have no sense of morality as we see it.
Mora treats his champions very well, but also has a nasty side (listen to his voice when he impales Miraak).
As for souls being trapped in Apocrypha, that's not really Mora that's doing it. He doesn't actively keep you there, you do, through your own greed. Acquiring knowledge from Apocrypha is never done just for the sake of learning, it's always to do with gaining or advancing power. It's that obsession with power that gets you, not him.
In the end, I think it's fair to say that even if he could be good or evil, he's only as good or evil as you yourself are.