Blue Lagoon will not take reservations if you list you are arriving by cruiseliner, as they have a contract with the cruise companies. It would require you to say you are staying on the island somewhere in order for them to allow you to visit blue lagoon.
Based on reports you could easily say you are staying at a local hotel for pick up and not have any issues. What I do not know is if there was an issue, like one of their ferry boats was broken midday or something and they only had so much capacity. I could see that scenario and all cruise guests get on the remaining ferries in order to meet the cruise ship departure times. Then on the subsequent trips, they would have Bahamas guests (of which you said you were one) because if you are staying on the island, you have less issue trying to get back to your hotel, and all you would miss would be a dinner reservation, not the rest of your vacation.
I hope others who have actually been to blue lagoon can chime in for you.