That doesn't seem to make sense, if you fly Elal regardless how you booked it you sould get points UNLESS you got points from Delta instead.
Quote from Elal website "Points for flights with partner airlines can be earned in only one frequent flyer account. Therefore, you must choose whether to earn them in your El Al Matmid Frequent Flyer account or in the partner airline’s frequent flyer account, as double earning is not allowed".