That reasoning makes me uncomfortable.
Sure, the agent is only human, but considering the seriousness of his post he should be sober and in control when in public, even when not physically protecting the President.
Anything else would reflect poorly upon his character.
It does make some sense. What kind of judgment was he using when he suddenly deplanes. This is post-911. This is high alert. The flight attendant had to be extra careful. Especially since he was an Arab looking man (I'm assuming.) I'm sure the new security procedures required her to look at his seat to see whether he left any suspicious parcels behind. She finds a history of the Arab world. Red flags are raised in her mind. She immediately notifies the Captain. He decides to doublecheck the guy's paperwork. Had the Agent not deplaned, probably the paperwork wouldn't have been scrutinized. I'll just add one last thing. Don't you think that this same agent and all of our President's agents do racial profiling while scanning crowds every day?