The primary reason for the ability change was probably to nerf it like so many other Pokemon because they thought it was too powerful (for example Talonflame's hidden ability used to give flying type moves a speed increase of one whenever in gen VI, but now it only gives flying type moves a speed increase of one when it's HP is at maximum), or it could be some person said "Why does Gengar have levitate if its feet touch the ground?" Game Freak: "Your right!", Game Freak used Nerf! It was super effective! Plus there are lots of Pokemon that levitate yet don't have the ability that take damage from ground type moves, like Klinkklang or Magnezone.
