Flight Manual Part 1 specifically states, "A properly completed E-2 form indicates full compliance with FARs (Federal Aviation Rules) and Company policy." If the Captain had allowed this passenger to board with improperly completed E-2s, the Captain could have been subject to FAA disciplinary action to include a fine, as well as suspension or revocation of his pilot's license.
FWIW, I can't stand AA. I've flown them a few times, and the experience has always been lousy. That being said, what kind of a USSS agent tries to board a flight with BOTH a) a gun and b)
less than immaculate paperwork??. Forget AA's behavior for a moment, that agent is a bloody boob. If he can't be bothered to ensure that his paperwork is perfect then he darn well ought to have hiss happy heinie fired.
And now that I think about it, since AA seems to be the airline of choice for sociopathic people with mass murder on their minds, I don't blame for being freaking paranoid.