Seriously, to get reasonable national borders in Africa you need to get in a time machine and do one thing. Eliminate the late 19th century partition of Africa and allow the indigenous states develop. If you can't do that, then go forward in time and make all European nations turn sub-saharan Africa over to a single multinationally managed UN mandate in the 1950-60's and establish processes for national/ethnic nations to be established by plebiscite that are unrelated to old colonial boundaries. Or, declare the entire continent off limits to the rest of the world and let Africans get about the business of nation state creation and expansion that Europe went through in the 17th thru 19th centuries. Bloody mess, but that's nation-building for you.
Africans are just as capable of being dicks to Africans as Europeans are. If not moreso- when you're living next door to someone hate tends to take on a far worse, more personal dimension.
The building of homogenous states generally isn't a pretty thing. Sometimes it works nicely, similar peoples gradually building a common identiy, more often than not though there's going to be suppression and genocide.
As to stopping the partition of Africa...well we historically have two examples there.
One, Ethiopia. Great. Worked out quite well.
Two, the Congo. Ah.....yeah......
There would doubtless be a few more Ethiopias in Africa, maybe Sokoto and the like. But the majority....its going down the Congo's route.
You have to stop industrial civilization arising at all to completely protect Africa, capitalism was going to spread its influence there whether imperialism came too or not.
Its really not as simple as just saying keep the Europeans out.