Can we let nature run it's course and let species that go extinct go extinct like they always have for billions of years?
Knowing that, we could selectively breed and engineer new species to fill the critical niches of species as they go extinct, so that the long-term viability of our own species and our allied species are never threatened.
The trick is understanding the point of certain threatened species as they are on the brink of extinction. It's hard to know if that species ever had an essential function if it isn't doing it any more.
So, then, whatever we choose to do—whether it is protecting species, ignoring them, or exterminating them—is, equally, letting nature run its course.