Saudi Arabia recently gave permission to Air India to fly via Saudi Arabian airspace on its route to Israel.

This is a  significant improvement to the India - Israel flight, as it shortens the flight time by about two hours.

El Al is complaining that granting India Air to fly over Saudi Arabia but not granting the same right to El Al is discriminatory and violates international agreements. This discriminatory policy gives India Air a significant advantage over other airlines. They have filed an official complaint with the United Nations and has been looking for help in getting Saudi Arabia 
source: Reuters

I hope the result of this will be Saudi Arabia opening up their airspace to other companies, including El Al, flying the Israel route, and not canceling the flyover rights of India Air.

The other thing is, El Al should get other airlines on board to protest the issue and file the complaint against this decision. It is not only El Al being discriminated against.