My firewall has 1 x vr NIC, 1 x rl, 1 x ath and 1 x udav, I've been running some variant of pfSense 1.2.1 for some months now and can't recall ever seeing similar interrupt percentages to what you see.
If you are curious to explore this issue further, perhaps you could take the interfaces out of polling mode and give the shell command vmstat -i to see interrupt rates on rl0 and rl2. Are these interfaces in promiscuous mode (possibly bridged with another interface)? Are they connected to a hub rather than a switch? Do you have something "new" happening causing more network traffic?