National Geographic is sensational jouralism? You mean like National Inquirer?
As with everything, there are degrees of truth to most statements, and I would agree that NG is more "sensational" than The Economist or a technical journal, but the article by Quammen was definitely not biased in the way many media reports have been. Besides, the death of millions of bats IS sensational.
As one who lives in a state where the extractive industries have ruled the roost for many years (and as one who is NOT a tree hugger), I am witness to the fact that man can definitely be destructive, even when he thinks his actions are harmless. We're just now starting to get much of our native trout habitat restored by treating the effects of acid mine drainage from the mining of high-sulfur coals and acid rain from burning those coals in pre-scrubber power plants. It will probably be centuries before the effects of mountain top mining are completely reclaimed by natural processes.
Man needs to accept that he can be destructive if he's not careful and use his brain to prevent unentended consequences. That said, blanket cave closures are NOT an example of man using his brain.