Perlmonks doesn't (hasn't for a while) put "index.pl" into URLs. It uses URLs like "?node_id=495872". Your browser is adding the index.pl. So stop using whatever link or bookmark that has "index.pl" in it and index.pl won't show up.
You could also add a "index.pl-remover" to your Free Nodelet via [href:///?node_id=`id`|outdex] (outdex), for example.