May I offer perspective as a Canadian gun owner (long guns as well as hand guns):
First: Yes the US absolutely cares about those who export guns and gun parts out of the country. It all has to do with ITAR. They do set up exit checks at land borders periodically to check just for this. They (DHS) has been known to camp out at parking lots of gun shows near the border and record Canadian plates.
Second: Gun laws, especially for handguns (restricted firearms), are very strict in Canada. We may only take our restricted firearms to a range, gunsmith, or border (for entry in to the USA for competitions). There are narrow exceptions for those in the armored car business or those who work in the wilderness. The charges this guy faces could mean prison time, or at least some hefty fines and a criminal record. Adding to his woes is that guns with barrels under 4.2" are prohibited.
Third: If he declared the gun to customs when entering Canada, he would of had the chance to fill out the proper paperwork or even surrender it. There are procedures for bringing guns into Canada. American hunters or those driving to Alaska do it all the time.
I think the pilot may have simply forgot the gun was in his bag. He may usually leave it in his car at the airport when he is away flying. It was not caught in the US because of the trusted crew member program, and he literally only realized it when he had to put it through the scanner for the first time in Calgary. It sucks, but ignorance is no excuse for the law, especially when in another country.