Story-logic would indicate that she is indeed innocent, and we as readers have evidence that someone has indeed been messing with her mind, but Harry doesn't know what we as readers know.

Harry's had 7 months to know that Hermione isn't a sociopath or a psychopath, that she's a very kind and moral and ethical person instead.

What's the prior probability he should therefore assign to this person, out of all of Hogwarts, to be the one to commit a cold-blooded murder on another 11-year-old kid? I think he's giving the hypothesis of her actual guilt pretty much all the weight that it deserves - effectively zero.