Like it or not, political parties are private businesses. The DNC was broke, and Clinton bailed it out. And like any investor in a business being saved from bankruptcy, Clinton had the right to do want she wanted to do with the operation. After all, she was paying the bills.
She not only took over the operation, she turned it into an extension of her campaign-fundraising machine, through which millions of dollars could be collected over and above the usual limits on presidential candidates. That was smart — and legal.