In general with food allergy problems the cruise line wants you to contact them ahead of time, then they also generally ask that you contact the head waiter to discuss the situation with him once you're on the ship. I would expect that for something like Celiac that they would indeed be preparing food in a separate part of the kitchen to avoid cross-contamination. In general, the cruise lines are pretty good with being able to handle these types of requests. Bringing your own food and having it prepared is probably going to be a bit iffier on ships (they may not want to bring food of unknown sources into their kitchen).
But I would say make sure you talk to the head waiter for your section, because they're the ones that are going to be able to help out in arranging things for you. (I know on some lines they'll bring the next days menu to you near the end of dinner and work out with you what might be reasonable for them to prepare for you so they can make sure they prepare it properly.)