From a strategic point of view having Light-Harry as a gullible ally is worth way more than having Dark-Harry be so knowingly. If the plot is to gain control of Magical Britain under one single leader who you puppeteer (him being embedded with your brain patterns and all) there'd be no sense in turning him dark now. The political strategist would rather:
Put Dumbledore in a bad position by allowing Harry to be the one to stand up for the students. Possibly in a way that humbles Dumbledore by the great "wisdom" of Harry, but meanwhile in a way that doesn't alienate Harry from Dumbledore's political allies before he's been groomed and positioned to lead them. A way to do this would be to present evidence that Harry would be able to deduct and present on basis of being the Boy-Who-Lived AND someone who actually thinks. It might very well involve Harry find out, and proof, that Snape burned the letters. Snape being a double turncoat means that he'd be an easy suspect. Quirrelmort already has good reason to see him gone (that's how he deals with traitors if you recall) plus it'd severely weaken Dumbledore's hold on the Slytherin part of Britain. Here the taboo trade-off is Snape's future who Dumbledore trades to keep the school.
Quirrelmort might already have been there for the duel between Hermione and Draco. Hence he'd have a memory of it and be able to pull that memory to a pensive. That memory would be enough to proof Hermione innocent. If this is the case Quirrelmort ends up distancing Harry from Lucius; which might be a good idea considering that Quirrelmort probably prefers to be the one in charge of the dark side and have Harry as a champion of the light. The taboo trade-off would then be Draco's father.
I see no reason to make Harry appear dark. Actually I'd consider that extremely stupid since Quirrelmort has obtained all the political power he could hope to and now knows that that is not enough. He needs both the wolves and the sheep.
Your reasoning makes sense, but I believe we're clearly supposed to understand that Harry's going over to his Dark Side was the premeditated purpose of Quirrell bringing the Dementor to Hogwarts in the first place. Quirrell's plan was defeated that day, more or less because of Harry's love (not romantic love, necessarily) for Hermione. That day Quirrell realized that to really turn Harry Dark, he had to neutralize those Harry holds dear.
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: