Babette et al:
Well it seems as though the new post "Captain's Table Manners" by the original poster, Andrew, clarifies matters considerably, and justifies even further the action taken.
As for the sweeping "just isn't done" mantra, I still say it's baloney, and if your father (who I assume is or was a sea captain) decided to give me an earful, I promise you I'd be up to the task of returning the favor. The captain is the master of the vessel and the crew, and a servant of the paying guests, just like everyone else who collects a paycheck from the line. If there is no redress from other quarters, it's perfectly reasonable to accost him. As for writing him on your personal writing paper and having your butler deliver it, please note that while we're very impressed at your ability to regularly stay in suites for steerage money, some others on the ship are blessed with neither suites, butlers, nor personal note paper. Some, in fact, don't even have windows.
In Andrew's case, the captain's table guests were evidently exclusively other officers, which makes the interruption even more justified.