Something's weird about what your IT folks are telling you. Traditional firewalls are for blocking incoming connection requests (ie, some other machine attempts to initiate a connection with yours), and on your company network you shouldn't have any incoming connections from anywhere outside the company. If you do, there's something seriously wrong with the company network's security. And connecting to an FTP server is not something that would require a firewall. You absolutely should not need a firewall on your personal computer while at work, no matter how secure the information on the company network is.
However, if the company has a requirement that you enable a firewall on your machine before they will issue you an FTP username and password, then you probably just have to comply, regardless of how little sense that makes. But again, your IT department is showing its ignorance. Your Mac has not just the basic firewall that your IT guys are claiming is inadequate, but it also has the well-regarded Unix firewall ipfw installed. It can be enabled and configured through the command line, or using a GUI tool like NoobProof or WaterRoof. If they tell you that ipfw is not adequate protection for connecting to your company FTP server, they don't have a clue what they're talking about on many levels.
If you already have login credentials for the FTP server, but you're having difficulty connecting to it, then that's a completely separate issue. If you've been using the Finder to connect, try a different tool, like Cyberduck, Transmit or Interarchy (listed in increasing order of capabilities).