I personally find little to like about Jamaica, and much of it has to do with the hustling one encounters in the ports. That said, we were treated very nicely on the maiden voyage of Freedom Of The Seas last June, when we arrived at Mo Bay. They rolled out the red carpet (really) and had a free concert for us at the pier. The port area was also tightly controlled with no panhandlers or other annoyances. Not sure if this is true for all cruises or cruise ships.
Mo Bay is indeed a place where one needs to keep their wits about them at all times. I'd never even consider doing anything other than a ship's tour there. Maybe I am being paranoid, but I prefer the situations where my mind can be at ease. Not easy words for a former U.S. Marine. We did take a taxi to Margaritaville - but that is a very controlled environment and safe.
I recall someone that I met on our cruise who did the zip-line tour. They loved it from what I remember.