I could foresee special crewing requirements for flights to Israel, flight and cabin crew of certain nationalities may prefer not to operate on this route, and the Israelis may prefer not to have them. There is always the possibility of an AOG with the crew needing to spend a day or two in the country, and service with a smile might be difficult for some CC when serving kosher food to ultra Orthodox Jews.
This is not unprecedented as American expat Pilots working for Vietnam Airlines weren’t allowed to operate flights to North Korea.