Fish is available at most WDW sitdown restaurants, but much less common at counter service locations. Some do have fish sticks/fingers on their menus though and there are a couple of fish intensive restaurants. Epcot has several "fishy" places: fish&chips place, Rose&Crown pub, Coral reef). There is also The Flying Fish restaurant on the Boardwalk.
At the resorts with counter service restaurants, they are typically set up with "stations", where one station will have burgers, another sandwiches, another pizza, etc. and some might have fish as one of the options at a station.
I would definitely ask at disboards.com and you want to go to the "disAbilities" subforum. There are lots of parents with food allergic children who hang out on that board who will know, or will know how you can get the info you need. They were very helpful to me in trying to find out the availability of soymilk for Amy before our last trip.
WDW takes food allergies very seriously though and generally works very, very hard to accommodate their guests. People report getting calls from the chefs before their dining reservations as the chef wanted to get more specific information about how to best address their concerns. Of all "family destination vacations" I think that you'll find WDW to be one of the best.
Beth, mom to older DD (8/01) and younger DD (10/06) and always missing Leah (4/22 - 5/1/05)