Prices are much more expensive at the airport. All places i’ve rented from in Yerushalayim, including sixt, hertz and avis all gave shabbos off (excluding insurance).
The best (and cheapest) way i found to rent a car in E”Y was through an American travel agency. The guy i use has gotten me cars for considerably less than others including free or cheap upgrades. His name is Yigal (I don’t even know the name of the travel agency) and his number is (718)338-0417. They will give you the exact amount it will cost and you won’t find any more fees when returning your car.