levo - 1:21 pm on Dec 7, 2012 (gmt 0)
Google will request every URL they have ever seen, forever.
It does, but it requests redirected URLs much more often. Redirecting URLs with index.php won't slow down Googlebot on those pages. Well, you're already doing it...
My website had kind of a similar problem, Googlebot used to hit non-existing pages more than existing pages (~5-to-1). I've fixed it by returning 410 before any canonical redirections.
My suggestion is to return 410, and make sure you don't have redirects (non-www fixes, query string dropping etc.) that end up with 404s.