You can inhibit I/O modules selectively in RSLogix 500. Missing modules that are inhibited do not fault the controller.
Go to the controller organizer, to Processor Status, and then the 'IO' tab. By default all the slot enable bits are set to 1; just set the one you want to disable to zero.
Remember also that SLC modules cannot be removed under power. I've seen a few ControlLogix users forget that the SLC can be damaged if the backplane is disconnected under power.