I am trying very hard to word this in as uncontroversial manner as possible, since my true feelings on this subject would be unpalatable to many.
I will settle for,
"Would the Israelis have been heard to protest as much if it had been a Palestinian diplomat who had been the target of this action?"
People who live in glass houses shouldn't fire bullets at kids who throw stones.
Danny, I am sorry, I will quite understand if you delete this answer and admonish me for a political response to a thread with political overtones, undoubtedly unintended by the initial poster and responders.
To answer the original question, the captain was completely justified in his action.
As a senior government Israeli official, in the circumstances prevailing, he should have been travelling on an aircraft provided by El Al.