I want to block access to \"sub/folder/index.php\", but not \"index.php\" anywhere else.
Order allow,deny
Deny from all
I think the simpliest rule is:
RedirectMatch 403 ^.*/sub/folder/index\.php$
RedirectMatch is in mod_alias module, that you certainly have. This does not implies mod_rewrite engine. Here we are simply telling apache that any access to sub/folder/index.php will generate a "403 forbidden" answer.
You can put that in a httpd.conf or in the root .htaccess (but really consider removing all .htaccess, it's bad, it's slow, it's sad that you do not have access to the real configuration files).