I've watched numerous home-made transom replacements fail 100% upon takeoff at the No-Wake zone, but the really bad jobs usually look bad to start with. If I saw potential trouble on a boat I'd at least warn folks, but had to let them launch unless it looked hazardous. Sinking isn't ever a light matter, as the boat owner must pay to have the hull and motor removed from the lake, and they are responsible for damages done from oil and gas spillage: fires, damaged shoreline, etc.. If you are skilled enough working with fiberglass then go for it. Anywhere else on the boat a glass repair wouldn't be such an important decision, so I wouldn't let a transom repair be your first fiberglass experience. Here's a handy site you might appreciate. Ignore the picture of the big boat, as all the advice applies to any glass boat. Click Here
I'd follow the advice to first know exactly how much damage might be there. You might only need to drill or scoop out a small area, once you get any rotted wood out, finding at worse your problem is simply a deeper & wider crack to fill and cover. I think it's not a good idea to replace the whole thing if not necessary, unless you have a professional do it. If all you have is a thin crack and caught it in time, then maybe all you need is some gel coat repair.