It's not the color of the skin that bothers me, it's the thinness.
The captain has the right ultimate responsibility to not fly when he feels it's unsafe...
Even before 9/11 pilots did not have to allow LEOs to fly with their weapons. Quite often the stewardess would give it to the captain or have it put in checked baggage. Sounds to me that this agent picked up an attitude during the Clintoon years.