There seems to be an assumption here that ecosystems are friendly places but they really aren't. Nature does not know best. The vast majority all species in history have been wiped out by their natural environments, many by their own genes.
All actions that we take to try to fix problems go on to create new problems. It's expected.
And, of course, this doesn't mean we shouldn't act, unless we have a good explanation now as to why the harm of a proposed course of action outweighs the benefits.
The alternative is to follow some kind of 'Precautionary Principle', which, as David Deutsch has pointed out, can only damage our ability to handle threats which we do not foresee.
Meanwhile, people's lives are in known peril from malaria.