It depends on the details of the accusations. A McDonald's franchise can't just put up disco balls and declare Friday evenings McKaraoke Night with cocktails. I'm sure MLB has some pretty strong language protecting the league from rogue ownership actions.
If MLB realizes that it has senior position to the owner in one instance, it will become attractive to look for other owners to exploit.
What is to be feared by bankruptcy? the team will just get a new ownership which is not the league. That was the major flaw in the GM takeover. The bond holders, actually owners, were stripped of their value in the company and it handed over to the govt. and unions.
It’s not much of a stretch for MLB to do the same thing.