Except that the entire reason for the conflict with the natives was that their home tree rested on the largest and most accessible unobtanium deposit on the entire moon. If gigantic mountain sized rocks of the shit were just floating around for everyone to see, then what the heck?
Another huge problem, if I remember correctly, is that the strength of the Meissner effect on a superconductor is proportional to its surface area, while its weight in a gravitational field is proportional to its volume, and any magnetic field strong enough to lift a mountain would be lethal to life as we (and Avatar) know it.
Face it, you can't rescue the ridiculously bad script and poorly thought-out scientific mumbo jumbo with handwavy references to background material. The script and story were just plain bad. Period. Anyone that isn't capable of switching off their brain just won't enjoy the movie.