The AA release doesn't "prove" anything; it's just as self-serving as any statement the agent might choose to put out. The real question regarding this incident is whether the pilot, or any pilot, would have treated a white secret service agent the same way.

If the airline allows a white armed federal agent on after filling out a form incompletely, but does not allow an agent of arab decent on in the same situation that is discrimination. I'm not making a judgement, that just the law. The pilot cannot make up separate rules for arab passengers. The "authority" of the pilot over the plane does not give him the right to violate an individual's constitutional rights.