You can not stop it permanently from running. But some strong mod_security rules from gotroot.com can help you prevent this in some extent. But I find it is more useful to block any script from accessing remote downloads. Applying such rule using iptables server wide, helps to prevent rapidleech/torrentflux from working!
In simple words: if you have no idea how to do that - ask your web hosting company to do that for you. Take it easy.
Did you check http://gotroot.com ? They have the rules in their site. You can have delayed rules if you do not take the pro-package.
I don't know name of software, just a guess CFX (not csf) you can find this software on CSF Firewall site, before you purchase first check all function.