Great to see you posting again.
Problem is that you know where the repair is and will always see the repair. I would try to make it as minor a repair as possible and leave it at that. No repair will completely hide the stupid actions of others sometimes.
I have used mini dutch plugs to hide defects and this may work for you. Consider using a combination of acuglass and very small wood plugs to hide the defects. If you had a 1/16" thick strip of wood that you could glue into the holes and then trim back before refinishing it might hide the repair. Cut into 1/16" x 1/4-3/8" x width of the hole tapered plugs, using a exacto knife. You have to have the grain going in the same direction and a very close color match. They do not have to go very deep into the hole, leave the top of the plug above the surface. After setting you can trim back and sand flush then finish. Color and grain orentation is very important but with care should be matched quite well.
Now if you have rust in the holes you will still have a black hole to fill. Other here might suggest a way to remove any discoloration. Cheap tacks tend to leave rust stains behind. Hope ypu are not fighting this problem also.
