I agree that her actions were egregious, but those weren't what the trial was about. The trial was about defrauding investors, not about defrauding customers.
I don't know if there is a separate trial about that, or if it's too hard to proof harm in an individual case, or if nobody ever bothered. Hard to get money out of a failed company.
Yeah, f@ck the customers. In the Capitalistic utopia of the USA, you cannot be allowed to embarrass the oligarchy, whether they work in private equity, the Fortune 100, or the military-industrial complex. They really are between a rock and a hard place with Holmes. She's obviously psychopathic enough to raise ungodly amounts of money, whatever the cost, but she embarrassed the wrong kind of people. So we wind up with a moderate sentence that means she will do hard time (to scare people away from outright fraud), but not too much (so she will be able to get back into the game after).
They could now bring that case without worrying that she'll get away without repercussion.