It's a problem without a neat solution, the way it stands in Automic today.
What we usually do is tell the colleagues of the soon-to-be-ex-employee to make a filter for all running objects of that user. Then, they "take over" (by right clicking in Activity Monitoring) all running activities of that user. Once we verify this has happened, we delete the user account.
Apart from this, we have gotten most departments to launch their schedulers and other top level objects with a blanket user account, one that is not bound to a specific user. An example would be an account called "SAP" or "FINANCE". Somewhat to my surprise, the auditors allow this in our case.
Either way, this only solves the issue for running objects. For change history, one still often finds "unknown/unknown" as the author of an object - this is unfortunate and something Automic ought to improve. But then, when you "transport" objects, Autmomic doesn't "transport" the change history anyway, so as more and more objects get transported between environments, that elegantly removes "unknown/unknown" by ... erm ... wiping the entire history clean. Wonder what the auditors would think about that ;)
Br,
Carsten