Well, one notable difference between your examples of eliminated pathogens is that there is a food chain built on top of mosquitos. There are plenty of animals that eat both mosquito larvae (ex: tadpoles, some fish) and adults (ex: bats, dragonflies). I don't believe there is a similar food chain built on top of viruses.

I agree that many of the risks are hypothetical, but I disagree that we can simply dismiss them. Taking a decent amount of time to understand cause and effect on ecosystems seems like a perfectly prudent thing to me.