The concept of Plugin looks very promising and a much required one, especially for those who keep experimenting with Themes and end-up with a bunch of Custom Fields of no use.
However, sadly this plugin didn't work for me. I've a Custom Post Type created named "Tutorials" a WordPress site and it has a custom field named "difficulty". This field got listed in your Plugin but when I attempted to delete it, it says no Posts found using this Custom field. This is a false negative because I cross-checked and confirmed that I do have Posts using this Custom Field, each one having value set too.
As mentioned, this plugin has the potential; just needs a bit of work and you'll be the hero for many. :-)