This error blocked VaultWiki's uninstall (appeared in front of you while you were performing the uninstall)? Or did you see this in the logs and the timestamp showed it happened at the same time as the uninstall?
If this had appeared in front of you, I would expect the request URL to be "admin.php?add-ons/delete". So it looks as though the scope "run-deferred" is a separate process from the original "uninstall" action. If this request was a redirect after the uninstall, then VaultWiki should not be able to run its code that JOINs vw_usercount, because the "uninstall" action already removed the event listener that does this and rebuilt the event listener cache before redirecting.
On the other hand, if this "run-deferred" action happened in the background (such as AJAX/JSON) or under a separate account while you were accessing the "uninstall" action, then this is a race condition that cannot be prevented on the code side. The only way to avoid cases like this is to change your add-on uninstall procedure: to prevent event listeners of an uninstalling add-on from running in a parallel thread, you should disable the add-on before accessing the uninstall option.