I like the Draco part, but the Lucius part seems a stretch to me. Lucius could have just stayed out of their way and let their bond grow, trusting to Draco to cozy up with a new power.
Actually, it appears more likely to me that this is a plot by Lucius to turn Draco away from Harry by setting Hermione in opposition to Draco.
But both Lucius and Draco are key to the resolution of this.
Mr. Hat is the trick for any Lucius Did It theory. Off the top of my head, I can't find a satisfactory Mr. Hat for this scenario. Snapes seems the only possible candidate.
We know Snape wants to eliminate bullies and chose Hermione as one of his tools to do so. Perhaps this is his latest plot to turn Hermione into the ultimate bully fighting machine.
Snape considers the magical government the ultimate bullies. He will offer Hermione the power to defeat them at her darkest hour after which there will be no turning back. After destroying the magical government Hermione will see her life as serving the singular purpose of fighting bullies.
edit: I was joking :P
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: