I agree that the reference to Sisko being "Black" instead of just being a dark skinned Human was jarring. It takes you out of universe for a moment. For that moment, I see Avery Brooks instead of Ben Sisko.
I also rememeber wondering how realistic it would be that he seems so personally affected by the Civil Rights movement. It was 400 years ago for Ben. Then again, there was the Benny Russel experience so that may make it seem much more "fresh" in his mind.