I don't think a carbon plug will be a big deal, I have a plug cutter drill bit set that will be able to cut a small tapered plug from a stack of carbon. I'm more concerned about the labor and resulting ugliness of building up a thick tapered patch on the outside.
He told me that epoxy without carbon fiber cloth is so flexible/compressible compared to the surrounding carbon, that it won't carry any of the load, and the edges of the hole will still experience about 3x the stress just like they do with an open hole. I was told that apparently the same is also true for a metal screw, as it has to fit fairly loose to have the clearance that allows it to be screwed in, thereby never actually loading up the screw in compression. I do then wonder about what if you epoxied in a metal screw, using epoxy with some sort of carbon dust in it to make it non-compressible? Or what about actually using a carbon fiber screw or threaded rod?
This stuff is fascinating, surprising, and counter intuitive- it makes me want to go pick up a composites engineering textbook so I can get a handle on what is actually going on with this stuff.
I also realize I'm probably overthinking this, after all the boat has been holding up fine for a long time as-is, as are almost all of the other unstayed carbon fiber mast sailboats out there with spars full of holes.