Harry doesn't know Snape was a Death Eater, a double agent, and the one responsible for delivering the prophecy to Voldemort!
Harry figured this out at the bottom of chapter 46, Aftermath Minerva McGonagall. Three people know. Dumbledore had to not learn first, because then he would only tell the one person who would set the trap (Snape) and only two people would know of the prophecy instead of three. So Harry correctly deduces that McGonagall learned first and told Dumbledore who told Snape who told the dark lord.
Whether or not Snape knows that Harry knows, we can't be sure. However, he does know that Harry knows who knows the prophecy. Given just this information he is aware that Harry could deduce that Snape was the mole who helped trap Voldemort. If it seems a little farfetched for everyone to be so smart, I will note that Slytherin House practically recreated the entire scenario, minus the exact specific details, of Harry's blackmail of Snape after one day. Snape would be used to this level of deduction and plotting in his students.
Actually, I think the Slytherin students reasoned rationally yet happened not to get the right answer.
Slytherin thinks that Snape can get away with being horrible because he's blackmailing Dumbledore, that Harry found out how Snape is blackmailing D, and that D now has to try to please both of them.
In actuality, Snape is horrible at Dumbledore's direction, in order that everyone think Snape is blackmailing him, when actually Snape is really on Dumbledore's side (chapter 77). (Or at least D thinks so, based on love-for-Lily.) But Dumbledore really does have...
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: