It's not the planes in the air that are having the problems, it's planes waiting to depart. Without a flight plan, a commercial flight can't take off. What probably happened was all the cancellations and refiles of flight plans out of ATL overloaded the system. Remember, the FAA does not always have the latest computer systems.
If a plane runs low on fuel, they can divert to the nearest acceptable airport that has fuel available. You just gotta let enroute ATC know that's what you are going to do.