Check your warranty and press the issue til Jeep caves on it, if they don't trade it in elsewhere and let them know they're not getting your business again. CSI scores are a huge deal and even a single negative customer service survey can seriously mess up a dealerships scores and they catch a lot of **** from it from the brands. Since you bought it there you should be able to do surveys on both sales and service and they know it.
Pretty much every new car has corrosion coverage in the warranty, even the Kias we sell do. Unless you're constantly beating on it then there's no reason for that much damage after 5k miles and a couple months. That's a defect in material or the paint job itself. Take it to another Jeep dealer if you have to and press them to deal directly with the local factory rep. You'll get a lot further with a brand rep than you will with everything going through the dealer. If you seem like you're going to let up they're going to dismiss it til you do and there's a decent chance they never submitted it to Jeep in the first place because their warranty pay on repainting the areas probably isn't worth it to them.
My two cents after working in a dealership service department for the last few years fwiw. Also you don't have a FSJ Cherokee, you have a WK2 Grand Cherokee. Correct section would be here: http://www.jeepforum.com/forum/f309/