Update:
I have it installed now. Yep, use:
mysite/mystore/filesafe.php?auth=mypass
to run it manually. Hopefully you won't get the 500 error, bheard. I think the script you were trying to run is just a component of KISS_filesafe, not the main script.
Annoyingly, my hosting company doesn't allow cron jobs so I plan to just do manual scans. The application_bottom solution seems less than ideal.