Here is the info I found on MouseSavers.com about current Military discounts at WDW resorts: MouseSavers.com - Disney World Resort Hotel Discount Codes & Deals
Active Duty and Retired Military with proper ID get 40% off "rack rates" at the official Disney World resort hotels for the following check-in dates: 10/21/07-11/3/07, 11/11/07-11/17/07 and 12/9/07-12/15/07. Limited availability - not all resorts will be available on the dates you choose. Use code FFR.
About BookingFor phone bookings, you pay a deposit of one night's room rate plus tax. No change or cancellation fee will be charged if you make your modification more than 5 days before arrival.You can book one room per valid military ID. Thanks to Small World Vacations for info.To reserve a room with the Military discount, call the Disney Reservations Center at (407) W-DISNEY or contact a travel agent who specializes in Disney travel, and request the specific offer code.
Best bet is to call and ask if this can be applied for your reservation.