Using fiberglass is a viable solution as long as it is done correctly. You MUST remove all of the rusted metal first, but you have to do this anyway if you are going to weld new metal in. Also the most crucial part is insuring that it is sealed up properly, you must make it so that water cannot get between the fiberglass and the metal.
You say that this car has bondo on it? if the bondo is already partially covering rust then the car is rusted pretty badly and you will have a lot of metal to cut out. However if the floors are solid then the car probly wont be all that much trouble to repair.