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.
I notice I am confused....
(I reread the Dumbledore conversation speculating that Quirrell was helping SPHEW in previous fights, and that can only be Snape helping.)
He could have memory-charmed if he didn't want to be known as working against SPHEW, but it is more likely that he was helping.
Now I do not have a good theory for who H&C is.
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: