Suppose that you want to allow JavaScript on Twitter and YouTube but stop JavaScript on every other website. How would you do that with StopTheScript? Here's the result that you want:
You deny access to m.youtube.com and mobile.twitter.com so that StopTheScript won't stop JavaScript on those sites, but you allow StopTheScript access so that it will stop JavaScript on other websites.
The problem is that Safari doesn't currently have a user interface to deny an extension access to a specific website. It can only allow access to a specific website. The trick, therefore, is to "do the opposite". First, in Safari, allow StopTheScript to access the sites where you want to allow JavaScript.
Then switch to the Settings app, where you can edit the site permissions.
Select the specific sites where you allowed StopTheScript to access, and switch them from "Allow" to "Deny".
Now you're almost done. Finally, switch permission for Other Websites from Ask To Allow.
If you ever need to add another website to the list, you can switch Other Websites from Allow to Ask, allow StopTheScript to access the site in Safari, then switch the site from Allow to Deny in Settings, and finally switch Other Websites back from Ask to Allow.
Obviously this workflow is not ideal. Hopefully in the future, the Safari user interface will add the ability to deny access to a specific website for a specific extension.