Your concern is very well taken. The point of the Civil Service Reform Act of 1978, which set up the modern structure for the U.S. whistle-blower law, was to separate out the agency that had management responsibility from other institutions, which would be independent of those duties and therefore be able to concentrate, without conflicts of interest, on merit-system ranks, such as whistle-blower protection. It would have to be separate. Otherwise, you'd basically be asking an institution whose primary purpose may be at odds with your own interests to be responsible for providing justice when you challenge its alleged abuses of authority. It just doesn't work.
I'd also like to just do a PS on this idea of courts versus informal administrative agencies. It's not a matter of one or the other; you need both. In a global system of justice, there is no substitute for due process and the right to confront your accusers and present your own evidence on the public record. You can't cancel that out. It can be done through administrative due process or through a public judicial system through the courts.
But Mark is right that many people can't afford to go through the full-fledged production of going to court and having the trial. There has to be an informal low-cost administrative remedy. The key is to have controls on that remedy. Without those controls, the delays can be just as bad or worse than in court. The secrecy can be absolute, unlike court, and further, they can turn into traps, Trojan horses. Further, they can actually create victims and investigate the whistle-blowers instead of the retaliation.
The problem with Canada's administrative remedy is that it is uncontrolled.