Things that make you healthier are legitimate input, not things that are "natural". Living naturally doesn't usually mean living healthier.
From another perspective, humanity has already transformed the Earth and ourselves. Ancient mosquito-borne infectious diseases and modern ones are fundamentally different systems. The pace of "natural" species evolution lags far behind the speed at which diseases mutate under modern population densities, nor is it designed for the life expectancy and quality of modern people. Vaccines are one of humanity's best answers to this problem. I see no reason to resist them.