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.