I also installed FreeBSD 6.3 and it detects both cards using the em drivers. It works for both, I tried using the net on both interfaces and it works fine. I have read that pfsense 1.2.1 will be based on freebsd 7 or freebsd 6.3. If this card is not supported by the current version, I might as well wait for the next pfsense release. I already downloaded the latest betas of 1.2.1. I will try to install it tomorrow and see if it detects both cards as well.
Regarding the throughput, I asked the question because this box will be handling traffic for an entire LAN of around 50+ users. I also plan to deploy one as a gateway router, handling our ISP bandwidth of 6Mbps while doing filtering, traffic shaping and IDS. Would this be too much to ask for the gigabit interface? :)