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.
From this I understand that she said goodbye outside the LC (in the magic side), then he entered, presumably closed the front door, traversed the LC, reached the back door that leads to the muggle side, and then he heard a whisper behind him. Unless the distance between the front door and back door is very short, if it was McGonagall she had to have gone to the trouble of crossing that long distance and exit the front door in the time it took Harry to turn around, or disappearing outright, or casting her whisper across the distance. While not impossible, none of that is very much in character for her, and Harry was distracted enough at the time not to notice.
I think it’s supposed to be a Clue, or at least a Mysterious Foreshadowing Event (TM). I’m not saying it was Quirrell, but the fact that he was noted to be there earlier seems like a hint. Although Hermione seems to have been an opposite influence to Quirrell, as Aris mentions below, remember that Quirrell is a very high level player. Much of that might have been intended as part of a complex Xanatos gambit, which can have more than three steps if you have access to prophecy and time-travel. “Make goverment crush hero’s girlfriend, hero crushes government” was suggested as a possible Quirrell plot, you need only prepend a “Make hero love girl” step to justify him being the whisperer.
(But don’t anchor on that one, plots that involve time knotting have plenty of opportunity for weird facts being explained as someone’s intent.)
From this I understand that she said goodbye outside the LC (in the magic side), then he entered, presumably closed the front door, traversed the LC, reached the back door that leads to the muggle side, and then he heard a whisper behind him. Unless the distance between the front door and back door is very short, if it was McGonagall she had to have gone to the trouble of crossing that long distance and exit the front door in the time it took Harry to turn around, or disappearing outright, or casting her whisper across the distance. While not impossible, none of that is very much in character for her, and Harry was distracted enough at the time not to notice.
I think it’s supposed to be a Clue, or at least a Mysterious Foreshadowing Event (TM). I’m not saying it was Quirrell, but the fact that he was noted to be there earlier seems like a hint. Although Hermione seems to have been an opposite influence to Quirrell, as Aris mentions below, remember that Quirrell is a very high level player. Much of that might have been intended as part of a complex Xanatos gambit, which can have more than three steps if you have access to prophecy and time-travel. “Make goverment crush hero’s girlfriend, hero crushes government” was suggested as a possible Quirrell plot, you need only prepend a “Make hero love girl” step to justify him being the whisperer.
(But don’t anchor on that one, plots that involve time knotting have plenty of opportunity for weird facts being explained as someone’s intent.)