Hi,
Temp tables will not automatically cleaned when you unchecked the interim run results option after workflow finished, as the temp tables are already created so un-checking will not effect anything. You need to ask end users to follow best practices.
You can create a utility workflow to list all workflows where this option is checked and send an email to admins/operators who can see this list in their inbox and take action, or inform end users to take action. This is not direct solution, but at least you will get an alerts email on daily or weekly basis.
Hope this helps. Thank you.
Regards