I think you're trying to look for a scandal which really isn't there. Turkish pilots fly into Greece and Cyprus, Greeks and Cypriots fly into Turkey (and go through their airspaces). While at my airline, Pakistani crew aren't allowed to operate into India (mostly due to potential AOG issues) and vice versa, they're allowed to transit the airspace of their 'adversary' with no issue. Taiwanese crew are allowed to operate into Mainland China and again, vice versa. As far as I'm aware, Ukrainian crew are still operating into Russia.
Unless restrictions based on crews' nationalities are imposed by the
state, airlines generally just crew as required. As for the individual's own conviction in not participating in such geopolitically sensitive flights, that's their prerogative. But given how UAE airlines have a VERY dim view on sickness, calling sick for those specific flights would be done at their own peril.
Fuel-Off