Currently there is no interface to delete private subscription or filters for users who have become inactive. The current available alternatives are

1. change the user password has to be changed to login as that user and make the changes, which is not possible in certain organizations.
2. Delete the entries from the filtersubscription table and clusteredjob tables based on https://confluence.atlassian.com/jirakb/keep-receiving-subscription-emails-from-deleted-filters-314450232.html which might corrupt data.

Administrators after changing the owner of the filter should be able to delete the subscription and the filter to avoid sending emails to the inactive users.