Cut it out, bend the replacement metal into the right shape and weld it in.. What could be easier?
Seriously, that is one of the hardest areas to work on not just because of the tricky bends but because when it's done wrong everyone can see the problems in about 5 seconds when they check out your car.
I have a '73 that rusted out on top all the way across, might be doing a new roof skin on that one....