I'm unsure that is an accurate description of the text.
You are more or less right about chapter 18. First, Harry makes his demand regarding Snape:
"Ah... he's also to stop reading students' minds."
Then there is this corresponding line within the compromise Dumbledore offers:
He will promise to only read minds when the safety of a student requires it.
We don't observe this promise actually being made. And we aren't even assured of when it would be made. A pointlessly legalistic take on the terms could be that Snape will make that promise at some point in his life.
But I think it's safe to say that the promise was made shortly thereafter.
I also think it is plausible that it has been followed. The closing of chapter 28 may be addressed by another quote from chapter 18:
"Common sense is often mistaken for Legilimency," said Dumbledore.
Hormone-addled children are ill-equipped for subtly. I think the more telling thing from the scene in chapter 28 is that Snape directly rejected her instead of leaving her pining, as he had been left pining. Previously he regarded the pain of rejection as the worst possible thing. But after his conversation with HJPEV, and I guess some introspection or whatever, he understands his acceptance of that rejection was better than eternal uncertainty.
(emphasis added as edit)
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: