I'll go ahead an answer my own question here: the issue was apparently driver related. On my third time installing pfSense, I manually uninstalled and reinstalled an updated version of the Intel PRO/1000 PT driver. After that, it worked without any issues exactly how I wanted it to. I'm not sure why that would be the case as even the updated driver was only slightly newer, but either way it works and is invisible to the host OS, which is all I need. I'm getting full gigabit speeds both ways with only 2ms more latency than I had before. I'm running Snort.