Well, at least in the case of Holmes, her legal troubles are not over. I'm not familiar with the details, but among the charges are defrauding investors. The trial just started on Sep 8th.
Several reasons.Just the lawyer fees to fight the SEC lawyers will be a lot. What they did could be worse than what the SEC found so far. Discovery process may be painful and lead to emails and documents to be published on the web. It will be a big distraction for the top brass.
Presumably the goal is to lower the number of three letter agencies investigating you.