Chapter 6:
"I am unlikely ever to forget it. Thank you, Harry, that does make me feel better about entrusting you with certain things. Goodbye for now."
Harry turned to go, into the Leaky Cauldron and out toward the Muggle world.
As his hand touched the back door's handle, he heard a last whisper from behind him.
"Hermione Granger."
"What?" Harry said, his hand still on the door.
"Look for a first-year girl named Hermione Granger on the train to Hogwarts."
"Who is she?"
There was no answer, and when Harry turned around, McGonagall was gone.
Chapter 8:
"No," Hermione said. "Who told you about me?"
"Professor McGonagall and I believe I see why."
While reading, I never considered this to be a mystery, or even a question.
FWIW I agree with your interpretation.
To take it further: McGonagall accompanies Harry to Diagon Alley, while (on Dumbledore's orders) learning as much as possible about him. She attempts to report to Dumbledore, but is speechless; Dumbledore may or may not be reading her mind, I don't know. Before this, he was happy to delegate the responsibility, but after this meeting, he naturally decides he'd better investigate personally. Platform 9.75 is the next convenient opportunity.
Yes, that's a lot of detail, but I think the story bears it out.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 81, which should be published later today. The previous thread passed 400 comments as of the time of this writing, so it will pass 500 comments soon after the next chapter is posted, if not before. I suggest refraining from commenting here until chapter 81 is posted; comment in the 12th thread until you read chapter 81. After chapter 81 is posted, I suggest all discussion of previous guesses be kept here, with links to comments in the previous thread.
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.) When posted, chapter 81 should appear here.
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, eleven, twelve.
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: