It's hard to say without looking at the boat. But if the only area of corrosion is the transom, it's definitely worth saving.
Heck, take a look at my jetboat, the bottom was badly corroded, and it was destined for the scrapyard. And here it is, several years later, I've taken that boat to places I would never dream of taking a regular boat!
That said, if the majority of the transom is FUBAR, then you might want to make a new transom out of some 1/8" aluminum plate. If I were going that route, I'd take out the old transom, clean the seams really well, and weld the new one in. Also, if you use the proper cross members made from square, or better yet, rectangular tubing, you don't even have to mess with plywood. For instance, putting a piece of 2x4x1/8 rectangular aluminum tubing across the top, which gives you an attachment point for the motor. Then some vertical stringers that are welded to the bottom side of that tubing, and run all the way to the floor.