ISA server, you mean the wanna be firewall thingy of Micro$oft, right? From my own experience, this thing is probably the worst firewalling application I saw, ever.
If you want to build a firewall, I would greatly recommend to make iptables rules by hand, without any GUI (out of your favorite text editor). You will _always_ get better results this way, it's way better if you need to make something in a production environnement.
If you really a GUI to make an iptable script, well... there is plenty around, search about fwbuilder, bifrost, firestarter, etc. A quick search on google will show you many.