If the holes are in the proper place for a bottle cage to mount, then why not put some bottle cage bosses on it. Especially now if you are repainting it. You can get braze on threaded bosses for cheap or make them yourself.. Anyone that knows how to light a torch should be able to braze them on the bike. If it's an aluminum bike, then riv-nuts or something else will be needed.
But if you are bound and determined to fill them, then some sort of epoxy body filler or other type of filler that can be sanded. Be sure that the top hole isn't in the way of the seat post regardless of which way you decide to go.