I think there is a very good chance that McGonagall is worried enough about Hermione, about Dumbledore, ... and won't check Harry's Time-Turner. She's not much into multilevel plots, she's smart, but too honest to live in constant suspicion.
Like she didn't think much about the consequences at the "war level" when she offered the fealty oath to Hermione back then in the Wizengamot.
She sees Harry in pain and traumatized, and she sees the immediate chaos, it wouldn't be very "in character" for her to suddenly suspect Harry and probe him like that.
It could happen because she learned to not follow her "role" anymore, but it still doesn't seem the most likely thing for her to do.
Moody or some aurors on the other hand...
I think that McGonagall has learnt enough to be suspicious of Harry, but she's still more circumspect than to call him on it in front of the whole school. Maybe she'll check up a bit later, and maybe in private Harry will be happy to tell her the truth anyway, with appropriate precautions. On the other hand, if he's decided not to tell her, then he'll arrange not to be found until it's too late. (When is it too late to check if a time turner has been used?)
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 116.
There is 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.)