I don't believe that one of the professors who have never appeared onstage in HPMOR could be revealed to play such a central role. Also not those who have appeared very marginally and have not been actually characterized (Flitwick, Trelawney). We also have no reason to attribute motive to one of them.
Minerva is, as you say, definitely innocent - because we have a scene from her POV.
This leaves, for practical purposes, only Snape and Dumbledore. It's not impossible for there to be a reveal of either one, but the obvious answer is indeed obvious. Nevertheless:
Snape is suitably evil, smart, and with reason to hurt Quirrel (he's afraid of him), possibly Harry (after their talk about James Potter), possibly Draco (private war against remaining Death Eater factions or bad blood against Malfoys), and no reason for Hermione that I can think of.
Dumbledore... It doesn't seem his style, does it? :-) Certainly if he take him at his word, he believes this to be a heavy blow against himself and Harry. He could have a motive yet to be revealed, but I don't believe this is possible in a story-management sense.
Snape is suitably evil, smart, and with reason to hurt ... Harry (after their talk about James Potter), ...
See, I have trouble with that, mainly because it's been established that he's still in love with Lily Potter (which is why Harry's advice was so cutting), and hurting her only son would fall counter to that.
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: