i can think of 3 ways. the easiest would be to grind it down to the metal with a 35 grit or so to put a nice "tooth" to it for the filler to stick, but i would use a fiberglass reinforced filler. Not just regular filler. the fiberglass will add strength to it and help it againist cracking. Bondo makes one and Evercoat makes one called "Kittyhair" looks like wet cat hair. it mixes like regualr filler. there is also duraglass, not sure who makes that one.
or you could weld a piece over the body line, but the heat would probably warp the crap out of it and they you would have even more work to do. I would avoid it.
i have heard about people using JB weld but never have tried it.