Experts debate when to jump the chain of command.
While a chain of command is important, it can't be supported blindly. I think there are more reasons for team members to jump the chain besides managers engaging in illegal activities or sexual harassment. There are some bad managers out there—sad to say—who aren't competent, harm their practices, and make their employees miserable. Sure, team members shouldn't take every whiny complaint to the owner, but there has to be a way for them to address genuine concerns about a problem manager.
Ideally, employees would speak to the manager directly, but that's not always possible or effective. And while I agree that managers should be supported—as every position should be if performed adequately—I also think team members need another option if the manager is legitimately behaving badly.
Now, if someone is just being a busybody, the owners will probably know. Hopefully they'll listen to the grievance, do a little discrete investigating, and then deal with the situation appropriately.
In either case, I feel that employees deserve more of an answer than, "she has her reasons." Team members should be treated as adults and allowed to understand the reasoning behind their managers' actions. People are more likely to buy into a decision if they grasp it.