There is a question of her violating the law. That's why she wasn't charged. The very question was, "does the presence of classified e-mail on the private e-mail server constitute a violation of the law?"
It was a violation of the law, there was no question of her violations, the only question was if the AG would charge.
They opted not to charge, the FBI opted, initially, not to charge.
Simple as that.
When you get a clearance and handle info, for us regular joes intent is never a option in mishandling info, either you mishandled it or you didn't, she didn't. When you are higher up though as always, laws don't apply to you.