I think that the comparison made for the COVID deaths (not specifically in your post, but in general) is a bit more complicated than that and should go beyond plain numbers. It should account for instance for the density of population (not for the initial cases but for the spread) or the average temperature (that could make the ground for a spread more suitable). And many more.
This being said, I agree that for Africa, Malaria is more problematic than COVID. But the future looks bright, doesn't it?
The future does look bright, indeed. While I'm yet to take any covid jab, I'll go extra length to get malaria c vaccine once it becomes locally available. I get malaria, at least, 3 times in a year.
Of course, the difference in infection and mortality rates could, and will most likely, due to a host of factors, some of which you have mentioned.