Having dealt with Billy Causey, first head of the sanctuary in the Keys, I developed a calloused ear from too much agenda presented as fact. Let's look at a few faulty premises in the article.
"thermal stress caused by climate change remain significant problems throughout the sanctuary" -not true. Ocean temperatures do not support the coral bleaching hypotheses. Dr. Eugene Schinn authored a paper which related bleaching to increases in iron which originated in the Sahara.
As for using sewer systems in the Keys, only the reality impaired support a sewer line that would have to stretch for over a hundred miles. And let's not forget that all the water needed for diluting and transporting that black and grey water has to be piped in from mainland Florida.
In the Sheeples Republic of FloriDUH, the inmates are running the asylum.
Coral bleaching and coral disease are two different things. Shinn's research was about coral disease. Coral bleaching is predominantly caused by temperature stress.
The main problem is still nutrients, whether from septic tanks, enhanced runoff (i.e., off of parking lots, not mangroves), or other sources. That means more algae in the water and less light for coral. Most of the elkhorn coral in the Keys (and around the Caribbean) has died off, and elkhorn is the most light-dependent species. Staghorn coral isn't in great shape, either.
http://www.nmfs.noaa.gov/habitat/ecosystem/AcorporaWorkshop.htm