Hi David,
Technically, SMOEAC is the console where you will be maintaining the Sites, Publications & Subscriptions. SMQS or SMQR will not effectively stop the middleware processing as SMQR txn is used for deregistering the queues and SMQS is used for deregistering the system. Even then, the BDocs will be created but it will be waiting in the Queue Scheduler for processing once the same is registered.
Based on the need, one of these options can be picked. Kindly let me know, what purpose of yours needs to be resolved?
Regards,
Karthi M R.