dAAvid, I read the section on carriage of accessible weapons. It is mostly about what LEOs must do. I missed the part that says "airlines shall accept armed LEOs who comply with these regulations."
What it does say is that the airlines must "Advise the armed LEO, before boarding, of the aircraft operator's procedures for carrying out this section." If the airline's procedure is that the Captain gets to decide then what in the regulations contradicts the Captain's action in this incident?
You say that the Captain exercised poor judgement. The regs say "the armed LEO must have a need to
have the weapon accessible from the time he or she would otherwise check the weapon until the time it would be claimed after deplaning." I understand that by parts (i), (iii), and (iv) of item (2) this requirement was technically satisfied. But assuming that you were the Captain and that it was your call, what, in your good judgement, was this agent's need to be armed on this flight?
I hope that the Secret Service does not try to bully AA.