Bellatrix is a puzzle.
Possible that he was actually in love with her, and that all the supposed torture was false memory charmed into her? I can't quite see how it would work, but my guess is that EY is a soppy old romantic at heart, so I wouldn't be surprised if somehow the relation between Bellatrix and Voldemort was transfigured.
Then again, maybe it wasn't Bellatrix at all. She was just being used again.
As DanArmak implies, maybe Quirrell is just driving a wedge between Harry and The Man. That's certainly useful, and plays into the current storyline of Hermione possibly going there. That was my first thought. Wouldn't that be a nice start to manipulate Harry into the Dark Side, a la the consistency bias? Also, it let Harry see first hand the torture, further alienating him from The Man.
And if Hermione gets sent up, I can't see Harry doing nothing about that, after liberating Bellatrix. Save Bellatrix and let Hermione rot? That doesn't seem likely.
However, didn't Hat and Cloak press Hermione that Harry would eventually sacrifice her for some higher goal? Somebody did that. Kind of a replay of Hermione looking to Dumbledore for justice, but receiving it from Quirrell instead. Maybe she gets disillusioned with Harry this time, and Quirrell rights the balance again? Maybe he wants to turn Hermione to the Dark Side?
The Bellatrix thing is a really good point, though. But it leads me to something else interesting - Dementors.
Maybe rescuing Bellatrix was just a diversion from the true point - seeing what Harry could do about Dementors. Defeating Death is central to Harry, Voldemort, and EY. Harry was extra sensitive to Dementors. Quirrell too. He asked for them at Hogwarts. He saved Harry from them. But Hermione said the Dementor's told her that Quirrell wanted the Dementors to eat Harry. And the Dementor told Quirrell that he knew him, and would hunt him down. Quirrell talked about "someone" attempting to destroy a Dementor. Death Eaters? A little joke from a guy who wanted to defeat death?
I would have to think, that given EY's values, the one transvaluation of values he'd want to achieve with his story is to get people to stop acquiescing and even loving death, and fight it. The symbolic crux of the story will be the fight against death. If so, betting on the Dementors as the issue for any plot point is a good bet.
Possible that he was actually in love with her, and that all the supposed torture was false memory charmed into her?
Charmed by someone other than Voldemort, I presume, after his death, and really they were two happy lovers all along? But then others (Lucius, Draco through him, etc) would have had quite different memories of the Voldemort-Bella relationship, and Harry would ventually hear about it when she became a popular subject of discourse after escaping from Azkaban. Everyone can't be charmed about this matter.
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: