There's nothing in this (or any other) addon that makes it survive factory resets. Sounds like in your case only the user partition was formatted, but addons are installed to the system partition. That's not a factory reset (one that also reverts to factory firmware).
Also there's no need to factory reset just to get rid of an addon. Just uninstall it.
Quote:
Originally Posted by frostschutz
To install, copy KoboRoot-MiniClock-*.tgz » .kobo/KoboRoot.tgz
To uninstall, set uninstall=1 in .addons/miniclock/miniclock.cfg
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It'll rename the config file to uninstalled-$date so you have confirmation it was uninstalled.