Hm... I don't use Gimp so Gimp specific answers are out for me, but that is a good point. I guess the real question is would the maker of the map have any color available? If so it would be naturally occurring pigment, probably mixed with water or some other solution to make it usable in a quill.

There is a higher likelihood that instead of color the creator would use different types of dashed lines some dash-dot, dash-dash-dot, that sort of thing to show the different lines without depending on color.