This type of cruise, throwing anchors in remote coral lagoons, etc, while using relatively small luxury vessels is becoming more commonplace. Have some friends here that went on one, they strongly suggested we do the same. Wow, I thought the larger all inclusives, like Crystal or Regent, were expensive.
I rather suspect in this instance the cruise line is telling the more accurate story. What probably happened was that even though the line had all the proper permits, authorizations, etc. when the ship pulled into the bay a few locals became indignant and began raising cain. There is a tendency for cruise line guests or tourists in general to assume all locals welcome us with open arms. I've lost track of all the discussions I've had with my coastal brethren up here where I espoused the positive virtues of a viable visitor industry, which fell upon deaf ears as they want no part of these huge "puker boats" in their commercial fishing waters.
Reminds me of the time when about 35 or so of us were first off our ship in Italy, early in the morning. We were headed for a tour of the ruins of a Roman amphitheater but our first stop was a quaint mountain village that had been turned into a tourist haunt. When we got there everything was still closed down but shop keepers and restaurante types were just beginning to stir, getting things ready for the day. Our Italian guide was talking away as we all walked throughout the still closed shops. All of a sudden an irate Italian came out of nowhere and ran into the middle of our group, he grabbed the arm of a lady and began berating her in Italian. Our tour guide went nuts and began screaming at the dude, also in Italian. The lady's husband didn't know what was going on but grabbed hold of the Italian's arm and held him off (The Italian picked on the wrong gal as her hubby could have anchored the defensive line of the Green Bay Packers). The lady shouted, "It’s okay, it's okay, I'm from New York". Turned out the Italian, who had been sitting off in an obscure corner somewhere, had mistakenly thought she took his picture or something.