I don't really buy that motivation. Even if Harry becomes Dark, it's unlikely that he will then instantly become buddies with everyone else on the Dark side. Instead, I would expect Dark Harry and Dark Voldemort to be bitter enemies, trying to be the sole ruler of the world.
The best motivation I came up with for Voldemort turning Harry dark is that he intends to possess him, or dispose of him and sustain himself on polyjuice. In that case, Quirrellmort might well take actions that look like actions intended to help Harry rule, in addition to moves intended to separate Harry from his allies, since Quirrellmort presumably doesn't want to side with Dumbledore, McGonagall, etc. (BTW, this is not the far-fetched theory I alluded to earlier)
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: