We're getting less of Harry's inner narrative than we did before the troll, so it's entirely possible that he's fully aware that Quirrell is almost definitely the big bad, but still wants him to live in spite of this.

After these latest chapters, though, I'm starting to think Harry's mind is being blocked specifically from anything that would harm Quirrell directly. Quirrell's perspective in chapter 89 says that he can't influence Harry directly through their connection, but Harry's "Dark Side" might be another matter. (How did Quirrell think talking to an Inferius like he was modifying its memories would help? He knows exactly how smart Harry is!)