These are all interesting questions! I would like to mention that it is important to remember when analyzing these scenarios that the world in which we live is very much a real-time system; seldom is it necessary to make decisions for "long time horizons" without the opportunity to adapt, change or update the decisions along the way.
For example, consider the hypothetical scenario where a cure for Malaria is spontaneously discovered and rolled out in Africa. Suppose, then, that in the few years following the end of Malaria, African population economists argue that an explosion is in play, to the point where the country cannot hope to continue to support itself into the future. In this scenario, I find it hard to imagine that even the most austere and strictly enforced population control program could not match the rate at which the population would increase due to the elimination of Malaria. Moreover, I would not expect that even in the hypothesized scenario, such austere measures would need to be enforced, although I will leave that to the economists and public health experts to figure out. I would suspect that most people would prefer a reality in which Malaria does not exist, but every family in Africa is only legally permitted to have one child, than a reality in which no restrictions on family size are imposed, but Malaria remains a top killer.
The point I am making here is that this is very much a real-time system, in the sense that action can be taken as soon as it is suspected that negative effects may be growing. If such negative consequences are to arise, we are not committed to a downward spiral without intervention. Furthermore, I would consider it unlikely that the rate at which the population would grow as a result of eliminating one of the leading causes of death is so great such that no intervention by the African people can keep the "net good" of the scenario positive.
(Let us suspend, for the sake of argument, the thorny path of quantification of good - suppose we use QALYs, with some simplified metric for human quality of life that is defined in such a way that makes comparisons meaningful)
