Yes. There is a reasonable chance that may go very badly. Malaria exists within a very specific niche inside the mosquito. It has risen to the top of the pyramid to establish dominance there. Knocking it from the pyramid, removing malaria from the environment that is the inside of the mosquito, will create a vacuum. Some other disease will rise to occupy the niche. Perhaps it will be harmless, or perhaps it will be worse. But what is true is that whenever a species is artificially removed another rises to take its place.