I'm afraid that I have to agree with Very Small Prophet...this story demands a little too much suspension of disbelief, even though it's well-wriiten on the whole and represents an intriguing "might-have-been".  For one thing, if I'm not mistaken, Remus eventually sets an exam in which the students in his class are required to demonstrate their skills againt some of the creatures Remus has covered in his class -- including a boggart.  Hermione publicly fails in her trial against the boggart, which takes the shape of Professor McGonagall telling her she's failed everything -- a lot of the people who are as priggish, pedantic, and controlling as Hermione is in canon are the way they are because they're secretly consumed by fear (specifically, fear of failure or something else unpleasant because they didn't Do The Correct Thing). If Hermione's boggart was so dangerous that she couldn't be allowed to confront it in Remus's class, this scene could not have happened. Your story also raises the question of why Dumbledore tells Remus that nobody is allowed to change time and yet obliquely tells Hermione to do just that.

The entire faculty has to have known about the time turner, unless you think they never discuss their students in the staffroom. "Miss Granger can't be taking Ancient Runes, Bathsheba. She's in Arithmancy with me during that period."It's true that Dumbledore imples that Snape doesn't know ("Unless you think they can be in two places at once.") but I think Dumbles is just mocking Severus. An enormous amout of mocking of Snape goes on in Book Three. Sweet thing to do to someone who's probably suffering from PSTD over being almost slaughtered by Remus as a teenager and never being allowed to talk about it.

Hope does, indeed, spring eternal. Too bad for Lupin, getting his hopes up only to have them vanished. Nice little story!

Ohhhhh, I like that explanation!  Nicely done! :)