If you are willing to re-blue and probably would have to re-blue the whole barrel to make it match you can sand them out if they are not to deep.

This is a renegade barrel that I removed the blueing and then I buffed out with the small surface rust with Scotch Brite pads... Then I re-blued it with cold blue applied to a hot barrel.

Certainly not as durable as regular hot blueing process but works really well.