I would ask the dealer to replace the headliner and fix the leak. They will probably need to remove your windshield and reseal it. Maybe even replace it.
Your windshield was probably not sealed good when it was built. Don't mention the windshield could have been replaced before you bought it. That would only give them an excuse to not assume responsibility of repairing it.
When he says they can't fix it, ask to speak to the factory representative. Tell them you paid good money for a jeep that still had factory warranty.
Be nice, and I bet they will fix it.
Let us know how you come out.