I don't think accruing mileage or making transfers between the two mileage programs is in the works. Right now the application to the DOT is purely for a code share agreement, allowing El Al to put their codes on JetBlue operated flights. Until now they were interline partners, allowing a passenger to purchase a single ticket with both carriers in the itinerary.
Having an alliance makes it harder to get DOT approval and I don't think it would be beneficial to either carrier.