Indeed this was what I wrote when the issue first flared up, and the fact that El Al refused to implement such a simple solution proved to me that they were not interested in resolving the issue, and were motivated only by hostility to religion. It would be very simple to implement both in prebooking and in airport assignment.
Even simpler, they could provide an explicit option to ask for seating next to someone of the same sex, and do the assignments that way. If there was enough demand on a particular flight they could even have single-sex sections. This is a very simple idea, that must have occurred to them but they refused to consider it.