If this is a murder-mystery arc, then Quirrell is the obligatory Red Herring. He had motive, means and opportunity, and all three were revealed in the first part of 6-part arc. The laws of fiction demand it not be this easy.
Yes, that could be exactly what Eliezer wants us to think, but in the end I think Quirrell being responsible would just be too normal, even if suspicion is temporarily diverted from him by making him a false red herring.
I think the point of this arc is not to leave you wanting for complicated answers to obvious-seeming questions, but simply to keep you on the edge of your seat waiting to see how things play out. It's about knocking down dominoes, not setting them up.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
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.
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.
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: