When is your cruise? We will be in Ocho Rios on 12/17 and do plan on getting off the boat. We will not be snorkeling, just because I think the snorkeling will be a lot better in Grand Cayman and Cozumel, so we want to do something different in Jamaica. But if you do snorkel, in my experience, it's not too hard to avoid sea urchins, since they are stationary, unlike jellyfish! (We once snorkeled in Key Largo through something that reminded me of the jellyfish scene in Finding Nemo, and it was terrifying! But somehow, none of us got stung.) My husband did have a run-in with a sea urchin in Aruba, and his thumb was red and swollen like an infected splinter for the rest of the week. But we had drifted too far into shallow water and he reached out to block himself from being pushed into a rock by the waves.... Anyway, I agree that if you did a boat tour, and just keep yourself a safe distance from the coral/etc (which you should do anyway) that you should be fine.
We are going to book a private tour in Ocho Rios, and are not planning to do any shopping, so I'll let you know how we do at avoiding some of the negative experiences you read about. I would hate to stay on the boat and not see Jamaica at all.