If you install the stock tune back into the Jeep before bringing it in there they can not prove you had anything done. In my honest opinion, if you are worried that a tune will void your warranty then you're better off leaving it bone stock and untouched. Wait till 2015 and do any mods you want then. If you buy a performance vehicle and plan on tampering with it then forget you even have a warranty. It makes it a lot easier if you just don't think about it, TRUST ME. I have 2500 miles on my 2012 and have voided the shit out of mine and being the first to do the work to it. If it blows up, well then, I guess it's time to save up for a nice 440 build.
Moral of the story, don't touch it if you're afraid to void factory warranties.