Brian, I agree that you can argue that humans are a natural part of the environment, and our impact is just another factor that contributes to the well-being or destruction of various sensitive ecotypes. But our rational decisions to preserve the reefs are just as natural as our neglect and destruction of them.
What I'm saying is, we're going to have an impact on the natural world because we are undeniably a huge factor on the state of the environment all over the world, and that's perfectly "natural". But it's absolutely in our best interest to do our best to mitigate the damages our species inflicts on diverse biological communities like rainforests and reefs (to name two overused but very valid examples). Rich ecotypes like that have so many natural resources that we have yet to understand, or in many cases, to even discover. If we continue killing species in these areas as quickly as we are now, we aren't just screwing the beetles and the ecotourists, we're screwing ourselves out of potential live-saving medicines discovered in those forests or reefs, biological controls for pests we have, environmental scrubbers to clean up our polluted urban air, and all kinds of benefits we can't even begin to imagine because we have yet to come across them.
It can be just as self-interested and self-serving to perserve reefs and rainforests as it is to do nothing and watch industrialization completely wipe them out. And it's no less "natural" of us to undo our human damage, as it is for us to inflict that damage in the first place, so I reject the idea that we're interfering with "natural selection" by trying to mitigate the rapid extinctions caused by our industrialization.
Nate