I don't see Snape's motives the same way. Here's why I think he's the obvious villain (if my above 'twist' is wrong :/):
We know he was behind the plot with SPHEW as the puppet master, and that it centered around Hermione. As a result of his involvement, the bullying situation escalated until Dumbledore had to end it. If not for Malfoy's involvement at the cafeteria, Hermione would have ended her anti-bullying crusade disgraced, embarrassed, and powerless. The fight with the 7th year had the potential to end things in this way with Hermione as well, but it did not due to sheer luck. It would be poor planning on Snape's part if he had wanted to help SPHEW in its fight. His presence at the last big fight is not evidence either way; he could have been there to bolster the slytherins or help SPHEW.
In any event, if we look at Snape's plotting in this light, there are now two people plotting against Hermione if H&C is not Snape. This does not make too much sense to me (from a who benefits standpoint) unless you consider Lucius as an option, but he loves Draco and would not plan something that might kill him.
Destroying the notes at the earliest opportunity is optimal, but the risk of being detected by Dumbledore OR Quirrell OR the Wards OR the Marauders' Map OR <competent time-turned investigator if the plan doesn't work> is significant if he tried to do so the night of the duel. His window of opportunity is not too large either, because Hermione would notice if they were destroyed too long before the duel. Perhaps Snape went ahead with his plan, confident in his ability as a Slytherin to maneuver the room full of shocked people into letting him search Hermione's room?
((Postscript: After I'm done typing all of this out, it occurs to me that I may have latched too strongly onto this theory and am now defending it because it's a pet theory and not because it's the best theory. I don't think that this is the case, but that's how pet theories feel 'from the inside' anyway. Bleah.))
Edit: Disregard due to reasons below.
The fight with the 7th year had the potential to end things in this way with Hermione as well, but it did not due to sheer luck. It would be poor planning on Snape's part if he had wanted to help SPHEW in its fight. His presence at the last big fight is not evidence either way; he could have been there to bolster the slytherins or help SPHEW.
I think it was pretty clear that he was there to help SPHEW. That makes sense given his memory charming of everyone involved and it was (very) heavily implied that he was helping them in other battles.
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: