The hunter in me says "shoot, shovel, shut up". Everything else in me says all things in balance. We barely understand how we impact ecosystems, let alone other species.
They were here long before we were and are as integral a part of the planet as we are, there is a heck of a lot of hubris to say that we get to determine what species live or die en masse.
My fear would be the lack of understanding regarding the connections within, and between, biomes. If we simply start exterminating things we have no use for, it's pretty easy to envision a point where we simply cause the collapse of an ecosystem by wiping out the mosquitos, which kills the dragonflys, which allows an overpopulation of a parasitic wasp, which decimates the bees, and voila, no food for us.