That was the last straw with me as a Gamestop customer when I saw that news. I was horrified by that news. I know most people at Gamestop wouldn't do that, but how do you know if your Gamestop that you go to doesn't? I quit going to them, and have since looked at other places, such as starting with the games official site's store, and moving on from there. Worst case scenario I would rather wait for release of the game and miss out on pre-ordering and hoping finding the CE in Wal Mart or another store that sells games.
Also it's not too late to get it from ESO's site if that's possible, my suggestion then would be first contact support, and ask them about your concerns with ordering the physical copy from them and still gaining the Early Access. I am pretty positive you should be able to cancel your order with Gamestop, order the physical edition of the game from ESO and have no problems whatsoever. I would still just contact ESO with these concerns first and make sure that I am right, and you should be good to go with no worries.