Apple doesn't do the legit unlocks, AT&T does. Apple will give you a locked AT&T phone. As far as I know, they don't even have the factory unlocked phones in the store. I had to order my unlocked 4S online last year because of this. The best you can hope for is to get is an AT&T locked phone replacement given to you as a "device-only" with no contract, which would require a restore to unlock, but I doubt they will do this. I really think you're going to have to buy another eBay unlock.
Let us know how it goes. I'm really curious if telling them it's unlocked will have any impact on the replacement - as in them refusing to replace it since and saying you voided the warranty because it's not an Apple/AT&T approved method. Are you planning on telling them that she bought it as a factory unlocked phone?
If it was me, I wouldn't risk telling them. It's not worth the $6.75 and trying to get a legit factory unlock in trade for an eBay unlock is pushing your luck.