I replaced the back 11 feet of my RV roof last year (2002 29 foot Coachman Class C). Bought a 12x15 sheet of roof plastic from a local RV repair guy and did the work myself. Pulled the whole roof off back about 12 feet, re-did all the wood and insulation inside, added a new fan, had to replace a lot of the internal curves too with custom wood. It probably took me 8-10 hours of work time and maybe $400 in parts, but I'm confident that section of my RV won't leak for a LONG time. I used eternabond around all of the edges and seams before putting the trim back on. We used it a few times this year in heavy rains with no problems.
So, it CAN be done cheaply if you have the time and ability to get in there and fix it yourself. That said, if the rot is inside the walls and they are too brittle to repair you might have some serious trouble.
Good luck!