Weld them. It's the only permanent solution. If you use bondo it will eventually absorb moisture, swell, and either fall out or crack. Leave it in long enough and it will rust the hole even bigger.
Using evercoat's "metal 2 metal" will last longer than bondo, because it's aluminum powder based it won't absorb moisture like talc based bondo will. I still don't think it's the right way to do it, but it will hold up a lot longer. Probably long enough that you won't have to deal with again, although it will come back eventually. You could also use lead if you know how to work it and the holes are small, that's probably the only way other than welding that would be permanent if done correctly.
I take it the holes from the studs being ripped out are already there? Because if they aren't you can remove the studs without making holes in the bodywork. The studs were just spot welded to the fenders, you can grind them off carefully and not make a hole in the bodywork.
