Found this post after i noticed this happening when playing a game and listening to music. Whilst you can’t mapping or disable joystick polling in the player,
If you copy these example input maps from AppData/Local/PlexMediaPlayer/inputmaps/examples
dualshock4.json
dualshock4-xbox-emulate.json
xbox-controller-windows.json
edit them remove all the binded controls from them and then save them to AppData/Local/PlexMediaPlayer/inputmaps that should disable the controller in plex for your xinput and dinput devices.