As long as there are only "rust bubbles" there usually is no need of replacing the whole roof!? Get rid of the paint to check how big the problem really is. When it's just surface rust it can be cured easily and won't come back (grinding, sanding, tinning, filling, painting). When it goes deeper you can just replace small pieces of the roof by cutting them out and welding new metal sheets in. And when the old paint gets sanded down, additional rust problems will be revealed.