It has been my experience that installing supported (no driver disk required) PCMCIA or Express Cards will load and bind the Firewire driver to the new hardware even if the driver was disabled for the built-in Firewire port.
In Windows Server 2008/Vista and above you should be able to use Group Policy to disable devices by their type. MS TechNet info: http://technet.microsoft.com/en-us/library/cc731665.aspx