I have found a major issue using your plugin with the Rezo theme by Themify.
The posts are showing the Category name twice, but the Category list has no issues when I'm in the Admin page.
In the category page (edit-tags.php?taxonomy=category) there is no duplicate entry. I see them double only when viewing the website.
You can see the problem here:
It would also be better if the taxonomy keeps the order even if the plugin is deactivated.
Thank you :)