Yeah so you mean it would be easier to replace the whole thing even though there would be more actual welding? I am also worried that patching it would increase the risk of the rust coming back at the welds or on the bits I didn't do but I guess that's to do with prep.The thing you need to consider is, how easily can you cut the rot out, then cut a repair piece from the new sill, then weld it in and blend it all together...
Personally I'd just replace the whole thing