He's shut down because he didn't get a permit - didn't go through the legal requirements for that piece of land. In a like manner if he didn't have his drivers license he could get "shut down" from being able to drive there.
I work with the endangered species act on a daily basis (for a multiple-use federal agency; disclaimer: the views expressed here are my own) - interpreting the effects of the action (in this case a timber harvest - of which I work on many), developing mitigation measures to reduce any negative effects of the action, and consulting with US Fish and Wildlife Service (USFWS - agency charged with enforcing the ESA).
From my experience, and I work on a lot of timber sales in endangered species habitats, mitigation measures can be developed to allow for win-win situations. Retaining portions of the stand, selective harvest, timing of operations, low-impact removal methods, replanting, road obliteration, etc. all of these measures might be useful for reducing the impact....maybe not avoiding an impact all together but reducing it.... As long as the activities don't jeopardize the future of the species, the USFWS will usually issue a permit (a "take" permit if mortality of individual animals will result) otherwise they will concur that although there "may be an effect," the effect will be reduced by mitigation measures and therefore the determination is "may effect, not likely to adversely effect." It may (will) take work to get to this determination (balance impacts to the species with being able to do the timber harvest) but I have never seen a project stopped because of it....but then I believe in (and work towards) balancing protection of the resource (wildlife, fish, plants, etc) with utilization of the resource (timber, minerals, etc.).