On my ispcp installation I have some starter files for apache sites not related to ispcp in this folder as well. I wanted to prevent deletion of them. But of course I could just move them somwhere else or rename them. Back then /var/www/fcgi just looked like a good place to store own php starters as well :)

But I can change above code to a simple delete as you suggested if you think a database query is not a good idea here :)