Firstly it's very easy to kill more than the entire population if you do it over a several decades - people get born, and killed soon after having children - then you as soon as their children had kids you kill the second generation.
Secondly - those estimations sound dodgy since Leopold's own records show he had more slaves than any of those numbers.
Thirdly - diseases played no role whatsoever. That was a factor in the Americas but it was never a factor in Africa since the major killing diseases Europeans brought were from cattle exposure and Africans ALSO had domesticated cattle. They were already as immune as the Europeans. If anything in Africa it was the other way around - the main reason Africa lost far less of it's population during colonization than the Americas did is because Europeans were confronted with new diseases they had no defense against. Tsetse-Fly and Malaria in particular.