It may be best to make the javascript execution configurable on a per-webapp basis, and disabled by default. When attempting to enable this, a confirmation box that explains the security risks of running javascript from untrusted sites should pop-up.
https://status.webex.com/commercial/status?lang=en_US is an example of a page that would be helpful to have Webapps test, but the content requires Javascript to be run before the important elements are present.
It may be best to make the javascript execution configurable on a per-webapp basis, and disabled by default. When attempting to enable this, a confirmation box that explains the security risks of running javascript from untrusted sites should pop-up.