It would be simple to solve that with a breeding population kept isolated. If the genetic modification wipes out the wild population, you reintroduce it.
For species that reproduce quickly, such as insects, this is reasonable.
That said the mosquito trick is that we can produce drones whose babies are also only drones with the same genetic malfunction. The number of drone-only mosquitoes expands exponentially until they are most of the males, then most of the population, and then in a couple of more generations, the population is wiped out for lack of females.
I'm not sure that this would work as well for a species that moves more slowly. Or whether we know how to do the trick for species other than mosquitoes.
This is also balanced by the fact that as far as we know, most any mosquito can fill most of the same roles in the food chains. We're mostly concerned with wiping out the few species that feed on humans and our pets/livestock. We could eradicate two or three species which carry West Nile, Malaria, Zika, Chickungunya, and a few other really bad diseases of humans, dogs, cats, songbirds, horses, and cattle that are spread by mosquitoes. Other species would still lay eggs, hatch, and get eaten or reproduce normally without threat to us.
Also note that despite the technique being proven in the lab, and the fact that mosquitoes kill a half-million people per year, we have not yet pulled the trigger and done it. Exactly for fear of the potential ecological consequences.
For species that reproduce quickly, such as insects, this is reasonable.
That said the mosquito trick is that we can produce drones whose babies are also only drones with the same genetic malfunction. The number of drone-only mosquitoes expands exponentially until they are most of the males, then most of the population, and then in a couple of more generations, the population is wiped out for lack of females.
I'm not sure that this would work as well for a species that moves more slowly. Or whether we know how to do the trick for species other than mosquitoes.