The fact that there are species that we don't even know about means there is still a lot to learn about life on Earth. It is generally a bad idea to aggressively mess around with a system that is not well-understood, that is what we're doing and this news items demonstrates how little we actually know about our ecosystem.
For example, I am appalled at how we still farm outdoors, where we have little control over pests and weather, especially given that our main methods of pest control tend to hurt us, such as through chemicals or through Monsanto-style genetic modification and patenting. We could begin to move in a completely new direction, and that is to create something like the Ultima Tower, as envisioned by Eugene Tsui.
It's clear that if we don't take grand steps towards engineering a sustainable future, we won't be able to survive a variety of calamities to which we are now exposed, and in that grand scheme, untold numbers of species dying, whether at our hands or due to our carelessness, is irrelevant.
http://www.tdrinc.com/ultima.html http://en.wikipedia.org/wiki/Eugene_Tsui
Why should we feel bad if a species comes and goes without we ever knowing about it? Isn't that expected and natural? Doesn't that happen all the time in the universe?