Unfortunately after several hours I was unable to disable the app via CLI. I was able to get nextcloud working again by taking a backup of the data directory and reinstalling it via the web interface. I did not end up needing to restore the data directory as it was not removed when nextcloud was uninstalled but I recommend a backup anyways.
Please be aware that you need to re-authenticate all clients/apps after this or you could run into fail2ban issues like I did.