I'm having a hard time thinking of evidence that would be stronger than the evidence against Hermione. Even if Harry saw her hex Malfoy with his own eyes, I wouldn't put it past him to suspect he was memory charmed. It doesn't seem like Harry is seriously considering the possibility that Hermione is actually guilty. Can you think of evidence that would cause him to raise the probability, not even to 50%, but to 5%?

And why does Harry believe in the innocence of Hermione? Take the outside view. It is the first crush of a child. Natural selection did not spit out such a thing as pure innocents.