I read H&C's frustration in 77 as genuine, which argues for genuine clumsiness. It does seem to have been decisive in getting Hermione to open up about her misgivings, which could argue back in the other direction, but that's not the only place in the dialogue where H&C seems to fit poorly into their role, and the others are all dead ends. In any case, failing to consider surface appearances -- when dealing with a twelve-year-old, however bright -- is really a fairly basic mistake, and one that I'd consider out of character for both Quirrell (who has a fine grasp of psychology) and Dumbledore (who's all about narrative conventions and would probably have gone straight to the fairy godmother guise).
I truly find it odd that no one considers that the evidence was given directly within the text.
..."Because you look incredibly dark and scary and suspicious," Hermione said, keeping her voice polite, as her wand stayed level on the towering black cloak and the faceless black mist.
"That's all?" whispered the voice incredulously. Sadness seemed to infuse it. "I hoped for better from you, Hermione. Surely such a Ravenclaw as you, the most intelligent Ravenclaw to grace Hogwarts in a generation, knows that appearances can be misleading
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: