From a purely utilitarian point of view, it may be difficult to impossible to defend the efforts that have gone into saving the pupfish, or a number of other endangered species for that matter. However, you’re ignoring the ecological perspective.
Society (to say nothing of science) has concluded that attempts to protect species is worthwhile, at least in part, because their role in our future happiness is unknown at the present time. The tiny pupfish may not do anything for us directly, but then again what the bald eagle or the grizzly bear provide by way of direct happiness isn’t exactly immediately obvious either. However, preserving pupfish habitat by keeping the water table up might, in the long run, have significant positive benefits. Lower ground water often has significant ecological consequences that extend well beyond a single species, can cause subsidence, etc. In addition, I have a feeling a great deal has been learned about fish biology as a result of this and similar efforts — knowledge that has likely been applied elsewhere to both humanity’s and nature’s benefit.
Finally, there is the happiness of biologists and other scientists to consider, to say nothing of the conservationists involved in attempts to protect this species. If we are going to make a utilitarian argument, then the happiness of everyone involved must be weighed. Here you tend to weigh only the happiness of those experiencing direct and immediate negative consequences. Saving species like this and learning how they function in their environment and why they live the way they do adds not only to the sum of human knowledge, but gives the lives of those doing the research a greater measure of meaning.