I would call and talk to them about that. At a minimum maybe they can reverse the original charge and re-charge it on your Costco card.
I looked up the Disney Visa perks (I didn't realize they're actually listed on a website!) and the perks there only say you have to have your card on your account, so I should be okay. If I find out there are additional perks for paying your cruise in full with the card I will definitely ask. Here's the information for anyone else interested:
When you check in online or at the embarkation terminal, enter your Disney Visa card as your form of payment for all onboard purchases.
On the ship, your "Key to the World" card will indicate that you're a Disney Visa Cardmember and eligible for the perks listed below. Perks cannot be combined with any other offers or discounts, including Cast Member, Annual Passholder, Disney Vacation Club or Florida resident.
Please mention these offers to ensure you receive the savings.
10% off the non-discounted price of 10-photo, 15-photo, 20-photo and all-inclusive
Disney Cruise Line digital photo packages
10% off select merchandise purchases of $50 or more aboard
Disney Cruise Line ships
10% off a
Castaway Cay Getaway Package, and enjoy snorkeling, bicycle rental, float or inner-tube rental at Disney's private island in the Bahamas, Castaway Cay
20% off a non-discounted massage or facial service aboard Disney Cruise Line ships. Available on port days only.