That's a really good reason for going after Stephen, but the same goes for Yuna. With Yuna you get the added bonus of maybe having two kils.
Maybe the person wanted to NK Stephen in order to prevent modkill and then NK Yuna Tomorrow Night? Or try to get her Lynched today? In that case he would've the alleged gotten bonus for both kills instead of for one.
One small thing I just noticed when Googling for the Hogfather: the Hogfather, teeth and the Tooth Fairy are linked in the same book (see link):
So, this could suggest that we not only have the Hogfather as a character, but also an assessin (Mr Teatime?) who was responsible for stealing all the teeth on Day 2. The specific win condition for this person could be to kill the Hogfather. Although that does not explain why the Hogfather (if he was responsible and is in fact a character) would go after Stephen. Maybe "Undead scare children, so kill Undead so that the children are safe"?