In VA, if the marina is sold or simply refinanced, an "environmental impact study" is required...this is causing all kinds of issues with good marinas wanting to upgrade or borrow against the property to do so...
Of course this in addition to all the COE, Fed, state and local permit process to do that same upgrade.
When the EPA comes up with a solution to barnacles, I would get excited (as would the Navy), but till then, they really should have no say so in the matter of cleaning boat bottoms...you are simply putting back what is calling your boat, a home...
Now scraping and sanding and such of bottoms - for sure it should be collected as best and disposed of as properly as you can.
With the amount of raw sewage pumped in to our water by city treatment plants, daily...I am really not sure that a few boat bottoms are of any real impact.