>> "so you click one button to whitelist the Javascript"
It's amazing how quickly 'click one button to be able to view this website' would irritate the hell out of anyone.
It's certainly an option for geeks or security freakouts, but not really an option for normal people.
Also how would a 'normal' person decide if a website is 'safe' to enable js or not? If you're the kind of person fooled into clicking for 'hot bartenders' and filling out a survey to get access, you're probably not able to decide if you should enable js or not.
The solution isn't to shift responsibility to users, it's to fix the browser flaws that allow clickjacking to happen.
The example given here should be a textbook easy to fix bug in browsers. It's a browser issue which should be high priority.
An iframe which isn't visible to the user, should not be able to receive input from the user.