Based on your use case there is no need for policy exception: once an entity is retired / set to inactive; all related controls are retired and will not longer be attested. This is a scheduled job running every 5 min OOTB. So if you maintain a decent CMDB, and use Entity Filters to maintain your Entity Types ("scope of systems"); SN will take of it for you. 

If you have such a large range of policy exemptions for specific "scope of systems", then just re-scope your entity types to assign more relevant set of policies against them. 

Policy Exemptions are meant to be exemptions 🙂