Evercoat Kitty Hair. Make sure the metal is really rough, use something like 36 grit sand paper, it will make sure the Kitty Hair gets a good bite to the metal and won't lift. It shouldn't need to be said, but make sure all of the rust is gone before using the filler, if it isn't, the rust will grow behind the patch and make it lift.
Another, non-fiberglass, option is All-Metal from USC, pretty good stuff, we use it to fill rust pits in thick sheet metal. As long as it has some form of backer, it should fill holes pretty well too.