All one 'needs' to do is disconnect the cable from the controller at the CTIS manifold under the truck (pax side, center) to fully disable CTIS. The system has no truck air pressurization when not operating.
To dispel a common myth, the most common source of A3 tire leaks is not due to the rim O-rings, but instead the round rubber grommet that seals the metal air fill stem into the stock A3 rim. These little gems rot out and leak, requiring the tire to be fully dismounted from the rim to replace. Lots of other threads and posts on this. The wheel valves seldom leak and they have a schrader (tire chuck) valve for manual filling already. One could remove the plastic fittings between the wheel valve to the rim fill stem and replace it with a reducing fitting and then install a schrader there, allowing removal of all the whell valve and other plumbing. It's 3/8" NPT as I recall - check my other posts and you'll see the fitting size.
Regardless of whether you remove CTIS or not, which is almost a 'Ford or Chevy' type argument, for reliability, please do make sure to disassemble each rim and fully service them by replacing the grommets and properly lube them up with Syl-Glyde cream (not spray) before re-installation and then torque the brass nut per spec. I replaced the rim O-rings at the same time, but this was more PM than repair. It will stop the slow leaks when the truck is parked, regardless of whether CTIS is there or not.