Harry trusts Quirrell less now than ever before,
Pish posh. That's what Harry tells himself, but what do his actions say? He's doubled down in favor of Quirrell. His self-reported unease is meaningless because the stakes are on the table and Quirrell is setting up the next round. Harry's resistance to bailing on one of his plans is proportional to the difficulty faced, and so next time around he will be even more in Quirrell's camp then he is now.
I'm still a little dubious of Harry's judgment of late (though it seems to be recovering), but I'm really surprised you're worried about his intentions.
I'm worried about his intentions because they suggest his morality is ill-tuned to the problems he faces. They will allow him to excuse himself all the way down to the bottom.
Update: Discussion has moved on to a new thread.
After 61 chapters of Harry Potter and the Methods of Rationality and 5 discussion threads with over 500 comments each, HPMOR discussion has graduated from the main page and moved into the Less Wrong discussion section (which seems like a more appropriate location). You can post all of your insights, speculation, and, well, discussion about Eliezer Yudkowsky's Harry Potter fanfic here.
Previous threads are available under the harry_potter tag on the main page (or: one, two, three, four, five); this and future threads will be found under the discussion section tag (since there is a separate tag system for the discussion section). See also the author page for (almost) all things HPMOR, and AdeleneDawner's Author's Notes archive for one thing that the author page is missing.
As a reminder, it's useful to indicate at the start of your comment which chapter you are commenting on. Time passes but your comment stays the same.
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: