http://www.nature.com/news/2010/100721/full/466432a.html Makes a good case for why eradicating mosquitoes will not be problematic. But every time there is a large scale intervention like this the side effects only become apparent decades after the fact. You mess with ecosystems at this scale at your peril. Even if we can't see any downside to this today that doesn't mean there isn't a downside. DDT looked pretty good…
We could try scaling slower. Say, eradicating mosquitos one 100 square mile block at a time, over the course of a century.