Of course. If you're committed down a path where your company is basically unfair to its employees, then yeah, transparency won't help.

A good example of transparency not helping is our sudden transparency about the activities of the NSA. Obviously that's not helping them. Though arguably it is helping us.

In a case where a company is intrinsically unfair to its employees and can't correct that, transparency would probably hurt the company but help all the employees - by sending a strong message that it's time to get the hell out of this crappy company.