Timber Framers Guild Forums General Barns and Traditional Timberframing Barn beam old mortice?#2

Plugging up the hole is a good start but adding a peg is probably unneccessary. Also by doing so you basically cut through the wood fibers and therefore you actually weaken the beam further.
I would recommend turning the mortises up so that they end up under compression when the beam is loaded.
If there are mortises on both sides you might have to support the beam at say midspan.