It IS fixable, and the dealer has NO EXCUSE...it is NOT a 'jeep thing and live with it'...I have a 2003 rubicon, had a 2000 sahara, swap softtop to hardtop and half doors to solid doors twice a year on the rubicon, and never had ANY leak problems on either vehicle.
Don't know ANYBODY in the area that does, either! Something is NOT fitting right and that's the plain and simple truth. Be firm with the dealer, and ask them for PROOF FROM THE FACTORY in writing showing that door leakage 'is a jeep thing'....and if they can't provide it, get the name and contact info on the Chrysler area factory rep and complain to HIM/HER IN WRITING and keep a copy of all complaints yourself.
NO ONE should have to live with this problem!