Most of the control functions are vacuum operated, and the few wires involved with heat and AC are going to be about the same no matter what you do. I think that unless you plan to do some major vacuum plumbing and reinvent the system with new vacuum valves, you're stuck with the stock controls. You might gain a little by replacing yours with those from a non-AC Jeep, but I think the wiring harness will be the same.
One thought (unsupported by anything but speculation) might be to see if you can remove just the fan control from where it is, and put it somewhere else. That would get rid of a few wires. Another crackpot idea I just had would be to attempt to move the entire control assembly to the area occupied by the ashtray, or the little tray in the console beneath it. YOu'd need to replumb the vacuum lines, which have no slack, but might otherwise be able to preserve all the functions. and be left with a nice big hole for all your other stuff. If you don't need a clock, consider also yanking it (or the blank plate to the left of the radio) - perhaps you could cut that out and install a fan that blows into the radio space.