Regardless of the actual damage in this instance, the CCC is empowered to restrict the use of public lands when they reasonably think environmental damage might occur. Parker/Ventana violated their rules, so the CCC sent a Cease and Desist, and they settled with Parker paying fines and Ventana agreeing to restore the area a bit. As a matter of public policy, the system worked as far as I can tell. As a matter of actual wrongdoing, I don't think we'll ever know — as you say, that would require a scientific study to discover.

As for Parker's absurdly long article, I dug into one of his more verifiable defenses and found that he's full of it:

"The media reported that this fish was an “endangered” species whose spawning ground was a creek near our wedding site. Yet a simple Google query of “steelhead trout” reveals that this fish is not, as the media had reported, a truly “endangered” species, but rather a fancy variant of the common “rainbow trout” that is abundant across North America — so abundant, in fact, that it is sometimes considered a pest species. "

Steelhead/Rainbow Trout is listed here on the NOAA website:

http://www.nmfs.noaa.gov/pr/species/fish/steelheadtrout.htm

This web page says that 1 "distinct population segment" is endangered, 10 are threatened, and 1 is a species of concern. And they kindly point to a report listing which is which:

http://www.nmfs.noaa.gov/pr/pdfs/fr/fr71-834.pdf

Lo and behold, the Steelhead along the Northern and Central California coasts are on the "threatened" list. So the "pest" bit was just empty rhetoric.