Then what in tarnation was AA thinking?! This whole thing sounds like a giant-sized charlie foxtrot with more than enough blame to go around. My biggest concern is that while all the parties involved are conducting a pi$$ing contest, passengers are be put at increased risk.
Pardon my French...
Correct. I don't believe they were thinking they were just trying to protect their Pilot without thinking through just what he had done.
No matter who you believe they either let lose a very dangerous heavily armed terroist into the terminal or they knew he was USSS and denied him boarding anyway just because he was Mid-Eastern.