First of all, you dont need a firewall on your ispconfig server as it will not give you additional security. On your server you run only services that shall be accessible from outside when you followed the perfect setup guide, so you would have to open these ports in your firewall anyway. But then there is nothing left to be blocked by the firewall, so there is no security benefit in running it and you can turn it off. A firewall is only usefull if you want to make services avilable to a internal network only without exposing them to the internet.
Back to your problem, if you want to run a firewall and want to use passive ftp, then you have to define a ftp passive port range in pure ftpd and then open the same ports in your firewall.