I'm implementing a version that stores that settings to the wiki. I have already implemented an interface to save stuff to the wiki, see [[MediaWiki:EditPage.js]].
Interesting, let me propose the following: Let's just use your EditPage interface to generate a .js page with a certain name as a subpage to the current users userpage, i.e. User:Blah/jsconfig_settings.js Create the page such that it contains executable javascript which sets the variables correctly, i.e. JSconfig.keys['blah'] = 'blubb'; etc.. To restore the saved value we'll just includePage() this page by default. Should give decent performance.