I think the yellow colour is a problem indeed. I'm not sure, but I think children growing up in Western countries easily identify themselves with yellow minifigures. I can't remember ever wondering why they were yellow (back then there were no licensed themes, but I had Playmobil as well), seems like I unconsciously accepted that Lego had to be yellow as all minifigures were yellow. I never thought of them being from a particular country, they were just people like me. But I did actually use the black heads of the ghost to have some "black" African minifigures for City of Pirate themes as well. It might be easier for children in Western countries to imagine that yellow is "their" skin colour, dunno.
The "Jungle" theme of 1999 comes quite close to an African jungle theme. But one runs into problems because of the yellow heads. As they are yellow, how de we know it's Africa and not Middle America? This holds for any theme by the way, the mining sets might represent Africa (we don't really have gold mines in Europe, do we), but it is difficult to imagine for a child probably. Even if you give them some masks / shields as in the Islanders theme (leaving aside that this is a stereotype), one might still think it's meant to be America and not Africa. So one would have to add lots of animals to make sure about the continent...
For a Safari theme, if all minifures have yellow skin, this might be understood as if TLC doesn't want to show African people. Remember that Playmobil has done nice safari sets recently with people of different skin colours. If TLC doesn't, then there might be some discussions (ignoring that minifigures of non-licensed themes are yellow always). Anway, I'm not that happy with Safari themes in this context, it gives the impression as if Africa's just a big zoo.
Another solution would be something like the Ninja castle theme. Say two different African tribes located somewhere in the past, or only one tribe fighting against some animal monsters / spirits. Playmobil has done some really nice things like this small set . Maybe give them semi-printed heads like the one of the Aztec warrior from minifiure series. But still, the skin should not be yellow. Again, this is might turn into the savage sterotype then.
Anyway, we have to keep in mind that Lego is mainly sold in Western (and Asian?) industrialized countries. We don't think much of Africa in general, do we? Leaving aside Egypt, actually I can't remember that I learnt anything about African history at school (I'm from Germany), except that they were later conquered by Europeans. We heard about Babylonians and other ancient cultures in Mesopotamia and lots of stuff about the Greeks and the Romans. That's it. Nothing about China / Japan / India. Mongolians insofar as they invaded Europe at some point. Nothing about Persia itself, except that the Romans fought against "them" and Alexander the Great conquered large parts. So it's no surprise that toys are as they are. I really like the Ninjago theme, but in the end it's just a stereotype thing. I would really prefer more realistic themes like the old castle themes (no dragons), which could easily be adjusted to other ancient cultures. But it goes rather the other direction, so many many fantasy elements, see the whole Ninjago theme (which is copied by Playmobil now), all the dragons / sceleton armies in castle themes, aliens in space theme.