*Babalu is probably significantly more malevolent and mischievous than OTL West African plague/death deities due to the presence of epidemics. A Female at the head of the Pantheon may not be out of the question, due to the reliance on the River Niger, and likely abundance of wealth.
I'd like to come back to this. Among the Yoruba and the other peoples who have Babalu (by whatever name) in their pantheon, the god of disease is also the god of healing and medicine - he makes people sick, but also makes them better. I don't think that would be the case with the *Malian plague god, because too many people
don't recover from pandemics. A deity who controls diseases that can destroy whole communities won't be associated with healing. On the other hand, the *Malians will notice that those who survive pandemics don't get sick of the same disease again, and that their resistance to *measles and similar illnesses works in their favor when invading armies get sick and they don't. So while the plague god will be regarded as cruel and capricious, he might not be considered entirely evil: he'll be the god that culls and tests the people to make them strong.
There might actually be two gods of disease. The first would be an older god, originally worshiped in the days before the plagues, who is much like Babalu: a god of disease, injury and healing, worshiped by physicians and invoked by the sick. The second will be the plague god, the one who makes the *Malians tough and strong but exacts his price first. Under ordinary circumstances, he would be propitiated but not invoked; the exceptions would be during time of war (when he might be asked to bring plague on enemy armies despite the risk to the *Malians themselves) or when a pandemic is in progress. Very likely he would not be named outside his temples. There might be myths about him that recall the story of the Assyrian siege of Jerusalem in 2 Kings 18-19, and stories like the one about Babalu being cast out for trying to sicken the other gods.
The god of death and the dead, of course, would be neither of these. Nobody would want the plague god to be in charge of the revered ancestors, not to mention their own deaths. S/he (probably he) would be a separate, more benevolent deity, and even if a *Malian dies of plague, he would be the one to be invoked.
Let's see: who else would be in the *Malian pantheon? At the apex, there would most likely be a supreme creator deity, a variation on the Mawu and Lesa story (female and male creators who gave birth to the gods and other living things), or both: these are common threads in Niger-Congo and Bantu religions, so they're probably very ancient.
Then there would be the big four: the gods of the sun (male), the moon/sky/rain (female), river (male) and land (female). The sun and moon are married, as are the river and land - the sun fertilizes the sky, the river the earth.
After that: There would be an agricultural god, probably female, having roughly the place of Ceres in the Roman pantheon. A rice god, who would also be the god of brewing and a secondary god of medicine - not a physician's god but an apothecary's. Possibly minor gods for other crops and for wild-harvested trees like palm. The three above-mentioned deities of disease, medicine and death. There would be a god of war, one of herds and pastures (who has somewhat menacing connotations for the *Malians due to periodic pastoralist raids, but is very important in the pastoralists' own pantheon), a storm god, a god of the desert (prized for his patronage of goods like salt, feared due to desert raiders) and, after ironworking is invented, a blacksmith deity. And, because this is West Africa, there would be The Drummer, a god of music, oratory and speech, who is also a divine messenger and a patron of poets and merchants.
There would be a trickster god in there somewhere - there nearly always is. The Drummer is the most likely candidate, but the war god would be an interesting alternative: an environment full of water barriers and islands would favor generals with a sense of logistics, timing and surprise. Maybe there would be
two war gods, one for the warrior who needs bravery in battle and the other for captains who must be wily in strategy and tactics.
Finally, the *Malians would have local nature spirits like everyone else, and would also have household patrons/revered ancestors: not gods as such but exemplars, and available to be asked for advice or invoked in family rituals.
Is anything missing, or does anything sound wrong for this culture?