Since Arabs are about a third of the Jerusalem population, and many of them are conservative and don't like mixed seating, my suggestion that a train, say of 7 cars as befits Jerusalem, will have 3 cars for general mixed seating, a Mehadrin car for men, a Mehadrin for women, and two more segregated cars for Arab men and women. I would put a mixed car at the front, then another in the middle after the two Mehadrin cars, and another at the end of the train. This will provide an even better separation between the Haredis and Arabs. If you wonder why Haredi cars should be towards the front and the Arab cars towards the back, well, Jews are in the majority. But I wouldn't insist on the privilege. Let the train go back and forth on the trucks (and not in a circular trajectory) so that the Arabs and Jews switch their relative positions.
Woman moderately wounded by firebomb thrown at her car in north J'lem (Haaretz)
from the article: Jerusalem light rail may have segregated men-only / women-only cars