The choice is not between making one species of mosquito extinct or doing nothing.

The choice is between making one species of mosquito extinct or using traditional mosquito control methods such as removing standing water. The traditional methods affect many different insects not just mosquitoes. Attacking specifically the species that are vectors for disease is the more ecologically sound method.

If we could remove the insects that carry disease then the outcome could be more insects overall, because people will be more willing to have ponds, etc.