That's why I'm so reluctant to think about the Hogfather, or a God being responsible for Stephen's death. Still options to keep open, but not likely.
I agree the Librarian might be possible, but we never see him do anything other than doing small mischief and eating and sleeping. And maybe working as Deus ex Machina in the end by closing a magic book, or finding a cure.
Nobby sounds like a better suspect for the thief, and a Troll or a magician for Stephen's death.