I would get a nail set and tap the staples below the surface of the wood. then I would drop several drops of water on the set and the moisture should cause the wood to expand over the staples. I do this on molding and it does cover it up.
If this does not work, then use a filler that is "STAINABLE" most fillers will not stain and they will actually stand out more. Tonge oil is a different question. I would experiment with some and see if it does blend in nicely. If it does not, then try boiled linseed oil.