It doesn't happen very often. It's very rare. It's a straw man that's often erected to argue against whistle-blowing.
If you look at the B.C. Health firings that occurred back in 2012, that showed what happens when you don't have an effective system in place. You have a kangaroo court and people being dragged over the coals—all for nothing.
An effective whistle-blowing system ensures that doesn't happen. If there is a malicious complaint or if somebody is just simply wrong, the system allows for an investigation to identify the problem and the inquiry is shut down.