It would be tough to get around it. Mikes yellow jeep is the first TJ I've gone through the dash on and I dont see how you could avoid atleast having to cut part of the duct out of the way. On his we just removed the section of duct work that runs from the back of the vent to beside the steerin column and will replace it with some flexible duct tubing. You will be able to keep the factory defrost vent because it's already ran with flex tube.
That's exactly what I did with my TOR weld in cage back on my '03 Rubicon. The kit came with the flex tube to replace. Vents worked just fine.