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.

Im curious about the food chain part, what happens to individual viruses over time, do they ‘die’ or degrade somehow?

We wouldn't have to destroy all mosquitos, though. Only a few species that are carriers of human pathogens. Once they are gone, other, benign mosquitos will occupy their spot, and will be eaten by the same animals as before.