As Mel said, the URLs exist and pages are returned when they are requested, so you can't do anything about that end of it other than ask the linkers to change the URLs.
The biggest PR split occurs with the 2 versions of the domain URL (not the index.php version). To minimise the split, make all of the links on the index page absolute - full URLs including the protocol (http://). That way, spiders will find only the IBLs URL for the domain without the "www." instead of 2 complete sites, and the PR from the
www.less links will spread through the www site.
Also, don't have any links within the site that point to the home page's pagename (index.php). Use only the domain URL or "/". That way, the domain URL is receiving all of the home page's IBLs, except those without the www from other sites.