I was just about to post that it's impossible to delete a taxonomy created by this plugin.
However, I just figured out how to do it. On the settings page for this plugin, remove the information in "name/slug" and "label" for the unwanted taxonomy, click "save settings", refresh the page, and they're gone.
It would really be great, for the sanity of future users, to have an easier option for deleting their taxonomies.
The thing that makes me keep coming back to this plugin despite its flaws is the option to disable the "post_tag" taxonomy. This is a very useful option.