Let's take a few big steps back. What version of Uninstalr did you use and what did you uninstall with it?
The program strongly suggests you to create a backup before doing anything. I'm afraid it sounds like you didn't do that.
Did you carefully review the list of paths Uninstalr showed you before the uninstallation started? Nothing is removed except those paths that are shown to you, and that are strongly recommended you to carefully review before you start the process.
The option to reboot the system is also there in the UI. If you don't want the system to be rebooted, you can uncheck the option. Windows Update jamming something doesn't sound like anything relating to Uninstalr.
