I also feel that that you have a battery / connection problem not related to the CD player .
The CD changer will make noises as it "wakes-up" after the power has been disconnected / interrupted for any reason . This is normal
if you really want to disconnect the CD then you can remove it by undoing the 4 nuts underneath the glove box floor , then disconnect the plugs / cable at the back of the CD . If you don't ever use it then perhaps leave it out and reclaim your glovebox for storage ?
