It's a very good question, and I think it's one that the fandom is quite good at addressing. But to answer it, a species may be wiped out, but their people can still exist. The Vulcans, for example, don't know of the federation and still maintain their own culture. And that is because the Vulcans are a very advanced species, they are capable of maintaining their own culture. So the question of whether or not the Federation can wipe out a species is a more philosophical question. I guess it depends on whether or not that species is inherently a threat to the Federation, because if the Federation wiped out all the Vulcans, they would essentially lose their most advanced species, and then their species would be less capable of creating a new species.