Yeah, she's right about the potions book--but she harps on it WAY too much. She still lectures Harry about the book even after Harry used something he learned from said book (the bezoars, or whatever the hell they were called) to save Ron's life.
The second thing you mentioned is actually Hermione's worst moment in the entire series, in my view. She gets upset with Harry when she thinks he's slipping Ron the potion, but earlier in the book, she helped Ron make the team by hexing the other keeper (Cormac?) during his try-out. Her anger at Harry made her look like a GIANT hypocrite, IMO.
Still, I get your point. She is seen to be "in the right" far more often than anyone else in the books.
Anyway, have you given any thought to what you're going to do next, whether it be expanding this story to DH, or a new story perhaps? I hope you keep writing either way, because I really liked this story.