Exactly how would it become 'apparent' that a jumpseater was turned down because he was an FFDO ?
Was the Captain taken to Guantanamo bay for questioning ?
And what would the FBI have to do with it ? FFDO'S are under the supervision of the TSA.
Have you or your airline management read lately the FAR that states the Captain is the ultimate authority on the aircraft, no one else, not the FFDO or Alpa.
I have several colleagues that have turned down jumpseaters over the years, not a squeak from our management / FBI / SECRET SERVICE/ NASA/ GHOSTBUSTERS.
As I mentioned earlier, If, as Captain you lack the basic authority to control your own jumpseat I wonder what else they have taken from you.
I give you 4 out of 5 Pinocchios for your story though, only 4 because I have heard better.