tedster - 10:35 pm on Feb 19, 2011 (gmt 0)
It is possible - but these days it's not usually so much, because Google now seems to handle common duplicates like this automatically. However, since you were seeing both versions in the Google index, there is a chance that full link equity was being split in your case.
What you also need to do for the maximum chance at seeing a benefit is make sure that no internal links anywhere on your site still point to index.php. If there are any, then change them to point directly to the domain root.