That is a bummer...
For the exhaust to overheat, there has to be something blocking the water feed to the exhaust which cools it down. Usually this happens when you operate the ski in too shallow of water and suck up sand and rocks, etc. into the fresh water cooling...or maybe a hose popped off due to a weak hose clamp or something. If a blockage, once the ski is able to run again, you will need to backflush the system and maybe pull some of the hoses off to see where the blockage is. I would recommend that you install a bilge pump to safeguard against this happening again. Check out
www.greenhulk.net. Tons of pwc info on that sight...and how to's on installing a bilge pump. Sea doo makes a kit that you could install as well...ask your dealer.