First off if you are so concerned about getting a security pass, why not call up Transport and ask them? That way you know you are getting the correct information.
You can fly into any airport in Canada with an appropriate pilots license and stop at the local FBO. You may need to show said license and be escorted to your aircraft to leave but it should be possible.
If you want to fly for an airline that operates out of the terminal at an airport, you will be required to have a security pass. The paper work is not all that bad although you will be required to provide info on your parents, spouse, and inlaws as well as your history for the past 5 yrs (where you worked and lived) The application must also be signed by the company you are working for. (you can't just go and get a pass, you must be working for someone) The security checks aren't done by TC, they are conducted by the RCMP and if there is a gap in your history (don't have proper documentation of your last 5 yrs) the application will come back to Transport as incomplete and you will be denied a pass.
As for your human rights crap, get real. If you have lived in Canada and can document everything, you won't have a problem with your pass. The problems have arisen from people who LEFT CANADA (mostly to the Middle East looking for the greener grass) and now want to come back. Its not impossible to get the information, just a few more hoops to jump through. To fly for an airline in Canada, possessing a security clearance is part of the requirements. If you can't meet the requirements then you don't get the job. I agree that it can be tough on some people trying to come home, but there is no Human Rights violation here