Dumbledore correctly surmises part of Quirrellmort's motivation for this arc's events: he's neutralizing all of Light Harry's allies. What Dumbledore hasn't realized, what is completely outside his hypothesis space, is that he's not doing so to attack Harry, or at least not as part of a plan to defeat Harry. He's doing it to remove all of Harry's support except Quirrellmort himself, so as to hasten Harry's consumption by his Dark Side. With only Quirrell to rely upon in the magical world, his conversion into Dark Harry will be much swifter.
Therefore, when speculating abut the rest of this arc, we must speculate about how this plan will neutralize the rest of Light Harry's allies: Dumbledore and McGonagall. Harry has already hinted that he intends to investigate Dumbledore the next time he sees Quirrell. Assuming Quirrell gets out of the Ministry without causing a scene, he will almost certainly have manufactured evidence that implicates Dumbledore, which he will show Harry.
So perhaps one of the "taboo tradeoffs" of the arc will be Harry successfully politically attacking the Chief Warlock of the Wizengamot, the Supreme Mugwump of the International Confederation of Wizards, the rediscoverer of the twelve uses of Dragons' blood, the defeater of Grindelwald, and the defender of magical Britain in order to get a first-year Hogwarts student off the hook.
That would leave only McGonagall, and Minerva would drop Harry in a heartbeat if he successfully neutralized Dumbledore. Thus his isolation from all except Quirrellmort would be complete.
I'm now considering your hypothesis about Quirrellmort instigating this to be the most plausible. I still do not believe it to have been his best move unless there's a good reason for him to turn Harry Dark. Besides I consider the option posted as a reply to Daniel_Starr to be more likely. Regardless, you get the up-vote for the better deduction.
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: