Hi Patrick
That is right the Option is to purge the User's Job assignments which would include other data from the job assignment such as organisation, position etc.
HR import has a jobassignment source from Totara versiont 10 that enables the deletion/update of manager information.
Removing suspended users from the embedded My Team report would require the embedded report to be modified with a filter added for user status so only active users can be selected.
Regards