I hate to see this happen. The hull must have had water lying in it for a long time for the trunk side to rot like this. It makes me wonder if there is not more damage elsewhere.
I am not a fan of Git Rot either. I would cut out the effected wood and splice in new wood. I do not think that the trunk needs to come out if what you show in the picture is all of the damage. If you are convinced that you cannot splice in new wood and the inside of the trunk is glassed, as recommended, you could scrape, grind out the bad wood and fill it back up with wood flour and cabosil thickened epoxy and glass over the outside and it would be more than strong enough. This would take a delicate hand with the grinder as you could grind through glass in a second. I would remove the centerboard and and put a backing piece inside the trunk and wedged tight against the side of the trunk that you are working on. Tape some plastic to the backer so that it cannot get glued in place if some epoxy happens to work it's way through the glass on the inside of the trunk. If you are careful enough to remove the damaged ply down to the glass, it will not be very stiff and may dish or get wavy. You might remove the rot in strips, say 3 wide and fill it in with thickened epoxy before removing the next three inch strip. I would remove all of the damage part on one side and just put in a new piece of 6mm ply. You can butt joint the ply as long as you cover the butt joint with glass tape. It is also important to remove all of the rotten wood and go well beyond where you think that the rot ends or it will continue to rot on the other side of your repair.