You could try Minwax "High Performance Wood Filler". This is a two part filler similar to Auto body filler. It takes a stain almost exactly the same color as pine. Trouble is, it sounds like your trying to avoid using a stain. The only other thing I can suggest is a colored putty. When I'm filling nail holes in finished wood, I buy several different colors and mix them to get as close as I can to the color of the wood.