I have safely capped thru-hull fittings with a pipe cap and filling with epoxy putty.
If your hole measures 2-1/2", you may not get a good fit with standard thru-hull fittings. A nominal 2-1/2" thru-hull will measure about 2-5/8 OD. A 2" thru-hull will measure about 2-3/8" OD. Epoxy on a backing block with the correct size hole might solve the fit problem.
Be sure to cut the thru-hull to the minimum length needed. The longer it is, the easier it is to break.
An actually fiberglass repair is the best way to deal with a hole you don't plan to use again. This is a good video showing the correct way to repair a hole in the hull.