My friend and I were discussing it a little more and I've decided that it's not entirely plausible, at least the way I had originally thought it out. The trypanosomes associated with sleeping sickness, specifically those in the species Trypanosoma brucei spend their larval stage inside the tsetse, and mature into their adult form inside their human/cattle/equine/camelid/antelopine host. Unfortunately, the trypanosomes once in their vertebrate hosts are able to adapt too quickly for the immune system to handle, so the idea that my friend had was that the trypanosomes would adapt to live out their entire life cycle within the flies instead of requiring the transfer between species. This way, the trypanosomes could possibly remain inside the former vector, the fly, and nature might select for those that can mature inside the vector instead over those that need another host to complete their life cycle. At that point, the trypanosomes may not attack the flies until they're in their adult stage, killing only mature adults. It may shorten the lives of the flies by a day or two, but it won't drive them into extinction. Instead, it would mean that the trypanosomes that cause sleeping sickness would become specifically adapted to fly hosts, and not infect humans/other mammals.
Although, there is the obvious problem that "sleeping sickness" is actually caused by a few different species of trypanosomes that occur in a number of different varieties of tsetse. So, if I applied this to one species of trypanosome in one variety of fly (specifically the morsitans variety, as they are the most widespread), I can see it creating an advantage for Africans in some areas of Africa, allowing for an increased human population and possibly the domestication of some native fauna (the common eland, specifically), but I think that by and large, sleeping sickness would still exist, and there's still malaria to worry about when it comes to empire-building in Africa as well...
