I honestly never felt that this episode was that full of African stereotypes. Yes, all of the Ligonians that we saw in the episode were of African ancestry, and I did see some elements of African culture on the planet, but there were also elements of Oriental culture, and Lutan's kidnapping of Yar was explicitly said to be similar to Native American behavior. Lutan's treatment of his wife may have been pretty cold-blooded, but there wasn't anything "African" about it. I don't know and I don't really care what may or may not have gone on behind the scenes in terms of Russ Mayberry, etc., but I really don't think there's anything in the aired episode that is derogatory towards Africans or anyone else. They never really came across to me as "barbaric", their buildings and technology seemed civilized enough, just different and perhaps not quite as advanced as the Federation's.
Looking back on it now, it's kind of refreshing to see an alien race without silly-looking forehead ridges or weird ears.