I think the idea is not to get rid of the "Supplemental Index", but rather to redefine what it is and how is works.
See the Google Webmaster Tools blog:
Official Google Webmaster Central Blog: The Ultimate Fate of Supplemental Results
Google is now (or shortly going to start) returning SI results more often mixed into the SERPs... without labeling them as such. The SI results are supposed to be deeper, esoteric queries - which typically has unusual content or content in other languages. How Google defines that is beyone me.
This shift will undoubtedly help some sites and harm others.