Silona will be going to wordcamp May 30th in SF to see about finding support in the wordpress community for a plugin!

You may find the digress.it plugin a useful starting point. digress.it is an evolution of the CommentPress theme that supports paragraph level identification and commenting of posts within Wordpress. digress.it is used on the http://writetoreply.org site, which was originally set up to support paragraph level commenting of public UK consultation documents. For an example of the theme in use, see http://writetoreply.org/jiscstrategyreview/