Snowden, being a contractor, didn't have whistleblower protections. In spite of that, he did escalate the issues he saw (Clapper openly perjuring himself before Congress), and was rebuffed. Since he leaked it, the courts have since found that the NSA was in fact violating the Constitution.

I would say the facts openly disagree with your assertation that if the whistleblower protections aren't enough, then it means the government isn't doing anything wrong.