From my reading, JKR simply doesn't like this character. It's the same as Doyle with Sherlock Holmes. Thus, Hermione is a badly written character which grates on many readers. I like her too, but for (what I suspect) different reasons.
My theory for her getting away with everything is that on the surface level, she's a model student. It would be unthinkable that such a person would be conniving, cunning, ruthless, whatever. And so, such a person, if they do something underhanded, could get away with it.
My prediction for book 7: Hermione will die. Poorly-written main-supporting characters do not usually survive.
Actually, from what I've read from JKR, Hermione is representative of her in the story. I really doubt she'll whack Hermione, but there's nothing to stop me from doing it....