There should be a cover over that but it probably wont hurt anything if you can't find one.
I think if you pull up the carpet and look at what you have then a bit of welding isn't that bad to get it back into shape. But that depends on if you are able and willing to weld on the car. A quarter of a single sheet of 16ga steel is all you need to fix it and look at the various guides posted around on what others have done. 16ga steel is cheap so at most you will be out 50 bucks and several days of work to get it solid again.
Here are factory measurements so you know where to put it all back together. Also a couple of old tires are all you need to roll it over onto its side so it is easier to work on. If you are careful it won't hurt the car, they are pretty light and easy to move around especially without the drivetrain.
As far as the body goes I would say use spray foam to fill the rockers in and sand it smooth and paint it. It is a Metro after all and it doesn't have to be a really nice looking one either. The only other option is to find side skirts off a swift and just cover the rust up
