There are a few methods that you could use to fill the pits after all rust has been removed. (some mentioned above)

1) Soft solder.

2) A hard solder such as silver solder or brazing.

3) Welding.

4) An epoxy body filler.

Only the welding method will allow reblueing, as you are putting steel back in the holes.
Silver solder and braze will blacken with brass black, but this will probably not match the blacking on the surrounding steel.
Epoxy filler is the easiest, and once smoothed down could be painted.

You might find a vintage cycle/motorcycle restoration service that could do the work for you, as the principle would be like restoring a pitted cycle/motorycle frame.