Like D said, there should be a sticker on the box that makes it abundantly clear that the customer is getting only the vanilla version of the game.
Perhaps the sticker should cover the term "GotY" and more stickers should cover any DLC claims elsewhere on the box.
Either GameStop provides this sticker to the gamebox, when re-sold....
...Or perhaps to avoid this problem entirely, this info should've been put on the back of the game-box already by the game publisher. Somewhere on the Game Box, it should made clear on there - likely the back-side of the box, where all the content is advertised and much of the legalese is put on fine-print on the bottom of the back-side of the box - that The Extra DLC Content is a one-time code to download all the DLC for BRAND NEW Versions of the game, not Used. This would solve the problem entirely, if they want to do the Re-Released Edition w/ The DLC Code gimmick.
Actually - better idea - publisher puts this info on the back of the game-box AND when it's resold by GameStop, they add their sticker to state that the ALL DLC code's been used. This way - ALL bases are covered, by both the publisher and the retail re-seller. No muss, no fuss - it's all their for the gamer to see plainly in front of them.
Again, for re-releases, I still think ALL Content should be placed on ALL discs. The reason a gamer would go to retail is likely to have the content on disc AND to avoid the downloading procedure.