The Deleted aged discovery maintenance task will do what you want: http://technet.microsoft.com/en-us/library/e555d7e3-3681-440a-82d0-319d2b4bdd08#BKMK_PlanMaintenanceTasks
Note however, that if AD Discovery picks up the system in AD again, it will just get re-created so you need to male sure you either enable the advanced filtering features of AD System discovery or clean up AD.
Site Server and Site Systems don't need to be discovered by one of the built-in discoveries; instead, ConfigMgr automatically generates a DDR for them by virtue of them being a site server or site system. I don't know if these DDRs are generated on a recurring basis though. Without the client agent installed and successfully communicating, no heartbeat discovery/DDR is ever generated for these systems so they should be subject to the maintenance task (unless the automatic generation of DDRs for site servers and site systems is recurring).
There is no reason not to install the agent on site servers and site systems if you want to manage them. I think it's OpsMgr where you don't want to deploy the agent to the management servers.


