The fact that Quirrel sometimes reverts to zombie mode suggests that Voldemort is teleoperating that body. Perhaps he has more than one body for that purpose, and simply used a different body for the breakin, rather than polyjuicing the first one. It would be odd that both bodies could assume snake-form, but I see no reason in principle why that magic wouldn't be transferrable.
If that's what happened, then the Quirrel body might still be alive somewhere. Voldemort might be alive (in which case he would return to Quirrel's body, and pin the blame on Harry), or temporarily dead, in which case Quirrel's vacant body might turn up somewhere.
This is plausible, and fits with my speculation that Quirrell's been Dementor-kissed.
On the other hand, Harry still feels a sense of doom when Quirrell is in zombie mode, which suggests that Voldemort isn't completely gone then.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.