There's no way to do this in default JIRA, and I believe this is actually by design. Deleting users can cause potential issues in the database, if I'm not mistaken.
Is your concern that these users are taking up user licenses? Really, as long as a user is set as inactive and isn't in a group that allows Application Access (thereby not using up one of your user licenses), you should be fine.
If your concern is that you have a hard time managing so many users, you should be able to filter down to just active users, or at least filter down to users who have a certain Application Access.
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