I've also used the Microsoft ICE application to stitch photos for panoramic scenes, sometimes used up to 5 photos. Not a bad app for something that's available free and fairly easy to use, intuitive. The only issue I envision is the speed at which you take the sequence shots. As long as the fish hold still and don't happen to be in the transition area to be stitched, you'll be ok. For a scene with corals only, should be no problem. A fast camera will help as well.
Here's a link to a photoshare from a recent trip to the backcountry. It contains a number of MS ICE stitched panoramic views. After having used ICE a few times, I now pre-plan many shots by taking several photos in sequence with the intent of making them easier to stitch. Most of the photos are single frames, but you should be able to pick out the panoramas... I think I have them noted as such in the narrative for each.
http://photoshare.shaw.ca/view/782036227-1268021602-65510/7820/