Other theories floating around are that Sam is now an angel, or that it wasn't Sam at all, but Lucifer. That one goes something like this: Lucifer never actually went into the box. If you'll remember in "Hammer of the Gods," Lucifer reminded Gabriel that he taught him everything he knows, including his little holographic-clone trick. Lucifer made himself appear to be standing over the pit to Hell, and Michael took the bait and fell into the hole with the "fake" Lucifer. The result: Lucifer's main nemesis is stuck in Hell and he can roam the Earth without fear.
This doesn't work.
The holographs are just IMAGES. Michael was PULLED IN to the hole because he was GRABBING something.