Modesty and a seat too far
The current seating spat aboard El Al planes reminds me of seating elsewhere in the Jewish world. When planning the wedding, the seating chart seems to rank as important as the Chuppah. Aunt Sophie wont sit with Uncle Benny who would be upset if he didn’t sit next to cousin Terri who is rooming with Sophie’s daughter. The brouhaha about certain men refusing to travel next to a female other than his wife on a plane seems easy enough to overcome long before there is a confrontation on the airplane. This on board argument helps reinforce the old expression that EL AL was an acronym for “Every Leaving Always Late” and is an unfortunate commentary on our ability to get along.
This is an issue for the men in question, not the rest of the passengers. The easiest solution is for men who have this need to be required to buy the seat(s) adjacent, if other 
such observant men do not also book seats. Preflight booking can ask if this seating issue exists. If the yes box is checked, then a new level of scrutiny is developed. If the box is not checked, there is not consideration. The seating chart can be developed using computer algorithms. Alternatively, sections can be set aside for the observant. If seats are not available, the section can be expanded or the plane listed as sold-out for that section. Maybe business class could be reserved for all women who find they are bearing the brunt of this bad treatment. Maybe we do a first come first served approach. The balagan that is the El Al boarding process would look much the same as it does now.
There seem to be a multiplicity of solutions available long before boarding takes place. For a land touted as among the technology centers, this problem seems far from daunting. To create an argument on the plane or make some passengers feel unwelcome seems to be the worst possible alternative. My guess if that if the airline were held accountable, a workable solution would be quickly found. Maybe the pending lawsuit is the needed catalyst.
Nisiyah Tovah!