They hadn't found that footage when they started shooting. Singer only found unused stuff from Superman I, nothing that was earmarked for Superman II.
Plus what the hell is more symbolic than our fallen hero ascending to the sky to reclaim his power? That's some powerful imagery. Having him lay around in the rock so a ghostly face can appear out of nowhere, pull a sistine chapel and we play the popeye music? That's a crap idea, seriously. It doesn't even have any movie logic working for it--because Jor-El shows up in the FORTRESS. He can't spectrally appear wherever he wants, even if New Krypton is made out of a crystal. It makes our hero passive, on top of that. You don't want Superman anymore passive in this flick, right.