RewriteCond%{THE_REQUEST} ^[A-Z]{3, 9}\ /.*index\.php\ HTTP/ 
  RewriteRule^(.*)index\.php$ /$1 [R=301,L]

This codes supposed to redirect index.php of folders to the base / of that folder. Now it just returns an internal server error. Any particular reason?

Does your server have mod_security.c installed by any chance?

Try adding this in the beginning of your htaccess:

<IfModule mod_security.c>
SecFilterEngine Off
SecFilterScanPOST Off
</IfModule>

No didn't work.

You know that search engines eventually figure out that '/' and '/index.php' are the same page. Both will end up with the same PageRank over time. In Google Sitemap you can even give preference to one or the other. Redirecting really isn't necessary anymore.

Best,

Justin

If you got 500, first of all look into your apache's error log