Personally I would cut out the rust! Replace the metal you cut out with new metal and weld it up solid,grind it down smooth then cut a piece of metal a little larger to go over the patches and weld them up solid then grind the welds to your desired look or if you are good enough welder you really will need not to grind the welds,all this in mind be sure to grind all areas to bare metal before any welding. The covers over the patched areas will give added strength to them.If you don't feel any added strength is necessary don't cover the patched areas.Once you get it the way you want it primer then paint all to match.
