I guess alot of this would come down to one question, are humans responisble for why they are an endangered species?.
If we are then we should probably put a effort into saving them especially if they are essential to their habitats such as bats and what not. If we are no way related to why they are going extinct such as a natural disease or predator in the area, then let nature take its course.
I think this has little to do with it. Ultimately we have scientists with a very robust theory, evolution. We currently have a situation of significant selective pressure, as evidenced by the increased number of extinctions that have occurred in recent times. We also have a number of species that we think are at risk for extinction. We are merely trying to determine if our understanding of evolution is sufficient that we can take species which appear to be unable to deal with the selective pressure they are facing and turn them into species that are able. You do this by looking at the whole equation of habitat, predator-prey, population, etc. It is the logical next step - practical application of the theory.
In order to do this, you need to pick species that are doing poorly, but with favourable equations. Meaning that you put your resources into the ones that you think require fairly small changes to turn them around. The ones that have the odds stacked so far against them would be fascinating to succeed with, but would take a long time, and be subject to too many variables to clearly show the benefit resultant from your efforts.
Benefits from this application may eventually be there for those with deep pockets, once the basic science is hashed out. Not that there aren't a lot of bleeding hearts out there to fund the research, but they are most interested in the cute ones, the large ones, and the ones most like themselves (mammals, social structures, etc).
Personifying Nature only is there to create a god out of the mashup of rules that exist out there and create another moral entity, there is no such thing as natural when speaking of disease or predators. Invasive species are simply the ones better adapted to their current environment. This is nothing more than finding a complex machine and trying to figure out how it works.