Reggie D, who designed the marine, was african american (I believe, going from the marathon home video) so it would be natural for him to draw the marine & bobs with black skin.
Another thing worth considering is the games colour table. When limited to 256 colours, divided into ramps of light and dark shades, giving you about 15-20 unique colours overall, you have to be pretty choosy about what colours you use. Brown is a more universably applicable colour than skin tone, so it could have been a necessity of technology and resources.
Craig Mullins is an entirely different entity in his own right, and as we know, his interpretations of the marathon universe were never gospel. They looked damn impressive though =)
//t