Whilst you can’t mapping or disable joystick polling in the player,
If you copy these example input maps from ~/Library/Application Support/Plex Media Player/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 ~/Library/Application Support/Plex Media Player/inputmaps that should disable the controller in plex for your xinput and dinput devices.
Source – https://forums.plex.tv/t/is-there-any-way-to-completely-disable-joystick-controller-input/171330/2