phranque - 7:10 am on Jun 18, 2013 (gmt 0)
you need to add a rule to your configuration that redirects all requests for the default directory index document to the directory itself with a 301 status code. (i.e. a url with a trailing slash)
that will provide the proper response to handle referred requests that include the index document file name in the url as well as search engines requesting to crawl these legacy urls.
linking internally to the canonical urls is a good signal of quality and intent but as long as requests for the index.html url resolve to a 200 OK response then your google index problem won't resolve itself.