You're actually making a very good argument that a "public marina" shouldn't even exist in the first place. That rationale should also be extended to just about everything else we've come to expect from government these days -- public schools, public hospitals, public housing, etc.
Possibly, but that's a moot point, because it DOES, in fact exist. As long as it exists, the Scouts have as much right to it as any other organized group.
Why can't a responsible adult within the Sea Scouts 'make a donation' buy taking on the slip lease himself -- ie. keep the Sea Scouts name off the paperwork. Could the marina then keep the Scouts off the property? I doubt it.