If its just a 8th" deep or deep but the affected area is really small, bondo is fine. To combat the bondo from aborbing moisture and causing rust, I use phospheric acid mixed with it. It will clean the surface from surface rust and if moisture is aborbed it will not cause it to rust. The acid will stop eating the metal once it reaches a certain pH balance, so you don't have to worry about it eating through. But the acid will eat at the paint though, so if the paints not gone don't worry about it.
The acid will actually cause the bondo to cure faster, so use less harden, and work quickly. You can always try to "pop" it out, but it will still leave some evidence of a dent, so you would still need to use body filler to clean it up.