It looks like a user upgrade tried to process while you were uninstalling VaultWiki. There is little we can do about cases like this, since most of the time it relies on a race condition where the process sees that VaultWiki is currently installed, but then VaultWiki finishes uninstalling while the process is still running. The safest way to avoid it with any add-on uninstall (not just VaultWiki) is to disable the add-on, wait at least 10 seconds, then run the uninstaller.
In the particular and rarer case shown in your backtrace, there is opportunity to catch the error, because it actually happened during the same request as the uninstall request, but the possibilities are really endless. I doubt any add-on would start every single method in every class to ask if an uninstall is taking place.
Still, I can see if we can wrap every query that might reasonably run in such a rare case for the next release. It will be a lot of changes to numerous files.