By default 'Auto Associate Parts to CAD Documents' checkbox is always enabled in Workgroup Manager during Check-in. But, user can manually uncheck the option. Is there a way to lock this preference from editing?
At the SITE, ORG, PRODUCT or LIBRARY, go to the utilities page and then preferences. Find Operation>Checkin Operation>Auto Associate upon Check In. Edit it set the preference to the desired value, check the "Locked" box, and press OK. All children under whatever level you set it at will be locked.