When I was flying VIP in the mideast, Arafat was on my plane once, as was the family of Bin Laden.
In fact, one of my ex-F/A's flys regularly for the Bin Laden family under contract on an ad hoc basis.
Flying these people was a fact of life, and I can assure you on these flights, the security they provided for their "principals" was far and above any I could have thought up.
In the case of this Comair pilot, I agree he has the right to exclude anyone (within reason) from boarding his a/c, however, on the surface he seems to have gone a bit OTT.
It would be interesting to find out what the actual situation was, for instance, did this gentleman show up with a police escort on the ramp and try to board throught the outside jetway stairs, or was he just another passenger who's status was pointed out to the Capt?
I do agree with what someone said, regarding the Israelli's should have provided (chartered) a private jet for this person, and then this all could have been avoided.