I like this idea. I think a couple more features could be really useful as well:
* Add a link to the highlight that would scroll to the coresponding title in the article
* A widget. Basically, in the metabox of the post you could choose something like "Show in Widget" and it would appear there instead of using the shortcode. On the widget page itself, the widget wouldn't have any settings, it would just have to be placed in the correct sidebar for the postmeta to get passed correctly and conditionally.
* I haven't looked at the CSS, but styling with !important should be avoided at all costs.

I like the way in which news sites are influencing the new development of WordPress plugins. ShareLines from FooPlugins is another good example of that.

Thanks for the write-up!