I doubt the issue is Facebook 'creeping [him] out', so much as it is that it's uncertain what exactly Facebook is going to want out of the deal. Facebook isn't primarily a games company, and it's even less a 3D/desktop games company. There doesn't appear to be any obvious motivation for Facebook to use this tech for its intended purpose, so the question becomes what exactly they do want Oculus Rift for.
I assume Notch is worried about those implications. Will Facebook start demanding that every Oculus Rift game have tight Facebook integration? Will Facebook do something strange, like have Facebook wall updates appear in the game world irrespective of whether it fits into the game? If I were a game developer, this'd creep me out too.