I'm guessing since you say the A/C isn't working that it has lost its freon so there shouldn't be a problem with removing all the components.
I will say this from a past experience dealing with freon, it is nothing to play around with, people say its illegal to release it into the air, not only is it illegal, but the freon can kill you in the way of suffocation. I was moving a freezer to haul to the dump last year and at some point one of the freon tubes snagged on a door frame, it instantly caused me to drop the freezer because I couldn't breath. Its very dangerous stuff.
Other than that, you can remove the whole A/C system if you like if you never plan on using it again. If the compressor is still good I would plug the input & outputs on it and hang onto it as that is the most expensive component to replace.