I'm glad that this plugin is still useful to someone
(Unless you are stuck with an old version of Sigil, the built-in Sigil function should now be just fine to use for all selectors and not just for classes).
Right now there isn't a way to bypass the GUI, but it should be fairly easy to add a preference in the json file to tell the plugin to just delete all the unused selectors without asking. I'll look into it.