Even if you make a mission using BAF &/or OMC anyone with CO or OA will be be able to play it - only the "Lite" package has somewhat poorer graphics. The only time you need to avoid using them is if you want your mission to be playable by those who only have A2/A2 Free (when you must not place any OA units, either). There should be no need to disable the expansions if you are not placing BAF or PMC units in the editor. The mission will only list addons (vanilla or 3rd party) that are actually used for the mission.
A Orcinus says you dont need to remove the BAF or PMC stuff its already present as a lite version. And you cant remove it either as it is included as part of the whole CO installation. If you dont want BAF or PMC units just dont use any, its that simple.