Index: wp-admin/network.php
===================================================================
--- wp-admin/network.php	(revision 13675)
+++ wp-admin/network.php	(working copy)
@@ -283,6 +283,7 @@
 // Construct an htaccess file.
 $htaccess_file = 'RewriteEngine On
 RewriteBase ' . $base . '
+RewriteRule ^index\.php$ - [L]
 
 # uploaded files
 RewriteRule ^' . ( $vhost ? '([_0-9a-zA-Z-]+/)?' : '' ) . 'files/(.+) wp-includes/ms-files.php?file=$2 [L]' . "\n";
Index: wp-includes/rewrite.php
===================================================================
--- wp-includes/rewrite.php	(revision 13675)
+++ wp-includes/rewrite.php	(working copy)
@@ -1683,6 +1683,7 @@
 		$rules = "<IfModule mod_rewrite.c>\n";
 		$rules .= "RewriteEngine On\n";
 		$rules .= "RewriteBase $home_root\n";
+		$rules .= "RewriteRule ^index\.php$ - [L]"; // Prevent -f checks on index.php.
 
 		//add in the rules that don't redirect to WP's index.php (and thus shouldn't be handled by WP at all)
 		foreach ( (array) $this->non_wp_rules as $match => $query) {