If I wanted to disable my A3 CTIS, I would remove the plastic tube & fitting connecting the wheel valve to the fill stem in the rim on each wheel. I would then use a plumbing reducing fitting to adapt the 3/8 stem pipe thread to a standard 'schrader' valve - the same type of valve used on tires. I think the schrader valve is 1/4 inch pipe fitting. You can get that valve at any car parts store for a couple of bucks. Then you refill the tire through the fitting. There is no need to remove or cap any of the remaining CTIS plumbing.
With that said, your issues with leaky tires is most likely NOT due to the CTIS wheel valves. 99% of the leaky tires are due to failure of the rubber grommet sealing the fill stem to the inner rim half. They rot & shrink, then leak. Unfortunately, to replace it you must split the rims and dismount the tire. The grommet is a couple of bucks from Erik. Labor is a solid few hours work with an engine hoist and a hefty impact wrench. There's a few posts on the topic and step by step instructions. Or you could pay a reputable heavy equipment tire shop to do it. There was a post last weekend from a poor soul who paid $$ for an obviously unskilled facility to do it. Frankly, I enjoy doing it myself because I know it's done right and I can PM everything else on the wheel -o ring, rust, threads, etc. at the same time so I fix it just once.
I'll bet that by replacing the grommet, you have no more leaks and the CTIS can stay stock, regardless if you use it or not. I had 4 of 6 wheels losing air - some fast & some slow. All 4 were fixed by installing new grommets and o rings.