Reality does not have to obey dramatic pacing.
A central part of Eliezer's worldview is that it is possible to lose, and lose big. An Al-Ghazali can come along and destroy the bright future of your society. A UFAI can destroy the bright future of your society. A Quirrel can destroy the bright future of Harry Potter.
If the fic is coming to an end soon, which I think has been implied, Harry's implosion and Quirrel's victory are a good place to end things.
(I should clarify that, by "most likely outcome," I mean "more likely than any other specific outcome," not "more likely than its complement." I think there's more than half chance that Harry will think of something, and I think ArisKatsaris has proposed the most likely way Harry will get out of this, but still think it's somewhat more likely Harry will fail than win that way.
What did Al-Ghazali do, exactly? Wikipedia isn't illuminating.
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: