Apparently the problem here is that missile can only be targeted during boost phase, meaning the range is limited by capabilities of the laser. Currently the aircraft would have to be very close to a missile launch in order to stop it. Therefore, the project was canceled.
Still, you have the 747, the power systems, everything else… Why not try using lasers in other ways? Maybe in an air superiority mission? What if they could shoot down air to air missiles or other aircraft?