As an experienced traveler, you probably already know this, but the only argument for using the cruise line excursion is that, if late, they will wait for you. If on your own, you get back to the dock late and the ship may be gone. Like a lot if other dive related risks, you just have to be comfortable with, and protect yourself from the risks as much as possible. That is, plan a lot of buffer time to get back to port after the dive. I agree with Roatan over Belize City as dive site.