While this might at first sound completely evil and without warrant, it does make sense for them to do this. Gamestop recently launched beta testing for their own game streaming service and so it wouldn't really make sense for them to start handing out codes for a competing service.
While I can understand the policy, have these people not heard of PR? Removing something from the box of a product that any other store has is pure madness. Not only that, but this makes you look bad no matter what way you put it. Sure, it might be free advertising for your competitor, but opening ever single copy and removing the code is seen by many, myself included, as pretty much stealing from your customers. Gamestop should have just rode this one out and had stern words with Square-Enix in meetings, but instead they manage to make themselves look like thieves to the public which is never a good thing. Whether you think this is a bad thing to do or not, Gamestop have handled this so incredibly badley.