There's no way either Voldemort or (for example, on the other side) Moody will possibly believe that it's safe to let a Slytherin (ambition!) who has been so high in the counsels of each side to run around free, perhaps plotting to stick his oar in at just the right moment to tip things.
Is there a hole deep enough to hide in?
That leaves allying with someone who can play on the Voldemort/Dumbledore level. There aren't a lot of possible choices. Maybe Grindlewald, freed from prison, but he was hardly trustworthy. There might be a really, really powerful witch in India we've never heard of, but that would be bad fiction writing. Who else is there?
If Snape can overcome his prejudices, the logical choice of ally is Harry Potter.
That is the logical conclusion your sympathies incline you to. I suspect that what Snape sees in HP is at best a future Dumbledore, and quite possibly simply voldy V 2.0 Why the heck sign up for being manipulated and a pawn a third time? Uh-uh. But this may entirely explain what the heck he was/is doing with SPHEW. He picked Hermonie as the potential future ally least likely to stab him in the back when convenient, and SPHEW as the bet least dependant on a single individual. (Because it is an idea. The idea that everyone can stand up and do the right thing.)
Without telling anyone. Which is hilarious.
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: