Whilst I don't think the index.php will have a direct impact on the SEO of your website it could easily have an indirect impact.
As CleverPhD rightly points out it is a pain in the *** to remember and type that sort of URL.
Not only for yourself but also for other websites and customers.
The impact this has is hard to quantify... If I'm a site in your niche and want to link to you does this put me off? What if I link to the wrong site?
Beyond that ending in index isn't as nice a user experience as just ending at the page name and ultimately its my belief that if you do whats best for the user you'll get good results from google.
