What you see on the outside is a sill cover (the painted bit). On the inside is the sill itself which is a structure integral to the chassis with little port holes on the external face. To some extent it doesn't matter if your sill cover is rusted as it's not structural. However the sill covers tend to rot from the inside out so they are a clue that all is not well internally if rusted.
So I'm not sure why your car has failed on rotted external cladding unless they can a) see through to the structural sill and that's going or b) there is a dangerous sharp edge that could hurt someone.
You can't replace the internal structural sill. So if that's holed a) it's pretty unusual and b) you can only really weld it up.
The sill cover is a different matter and is a quick job to physically replace. You'll struggle to find a decent pre-facelift sill cover secondhand. Let alone in the right colour. And welding a patch on it is going to be ugly.
You're better off buying a new one. These guys sell OEM parts and can ship a sill cover from Germany for about £140.
http://www.genuineautoparts.com/uk/
You'll need to get it sprayed. You'll get a better economy of cost if you get both sides done and sprayed at the same time.
You should also take the opportunity to drop the jacking points on the underside of the structural sill and clean and treat any rust down the whole length with something like Por 15. No point putting a shiny sill cover over rust. You may also find when you start digging that the sill end of the front and rear arches is rusted or at least in need of a spring clean to clear the debris out that tends to cause these issues.
If you look at my thread here you will see pictures of all of this.
http://www.zroadster.net/forum/viewtopic.php?f=5&t=44270