Permanently redirect http://www.seobrien.com/index.php to http://www.seobrien.com. Google search - 301 redirect examples. Make sure to double check all your internal navigation and update those links as well if needed.
I've never run into that before...always works ok for me. You could do the opposite in terms of the redirect - www.domain.com to www.domain.com/index.php. The basic purpose of the redirect is to not create duplicate content and have consistency in terms of your urls. Pick one and stick with it.