You should be able to make a dummy esp and stick your script into an associated bsa. That way, users are essentially turning your script edit on and off when they check or uncheck the esp. To tell the truth, it much cleaner that way than a full overwrite because the user can uninstall without having to search for the original script to replace it.
You can manually add files to the bsa if you want the pex in there too.
Edit2: P.S. if you haven't already, put it up on the Nexus. I was willing to give the Workshop a chance, but it somehow manages to take away control from both modders and users at the same time. It was a good convenient idea, but the Nexus is still better in almost every way. I uploaded my mod to the Workshop, but no way am I letting it arrange the mods I've downloaded
