They neglected to take his gun during this whole episode. No one ever drew a gun on him. Boy you sure dont require much of the pilot do you. Doesnt sound like they were seriously worried they he might be an armed terrorist past three levels of security. They sure didnt act like it.
Also note they didnt close down the airport. Every day this week there is another report of an airport being temporarily closed down because some luggage wasnt checked properly or someone made it pass security, or whatever. Apparently they didnt treat this case that way.
FAce it, the pilot knew the guy was likely an agent and therefore not a threat. He just didnt want him on his flight, perhaps thinking being armed he would make his passengers uncomfortable. Who knows, but if the captains and Airlines actions are what we are to expect when confronted with a serious security threat, then you wont get me on board a flight anytime soon.
I suppose the pilot should cook the food and fill up the gas tank too right. The pilot's job is to make sure the plane lands safely, and to make sure the cabin is secure...his job stops there.