I would try to install it with a normal PC that have two IDE port and then boot the CF into your Atom board. This might work, although I didn't test this myself. pfSense install all the drivers even if you don't have the hardware, the purpose of this is probably to allow you to add hardware to your router without having to reinstall. I prefer to sacrefice some MB to have all drivers onboard than having to reinstall pfSense everytime I have to add a NIC that use a different drive than the ones I had at the initial installation.
I just read on those Atom board, you should have SATA ports, get a cheap SATA CDROM and problem solved, but make sure the BIOS can detect SATA CDROM, most new BIOS can, but just be sure before ordering a new hardware.
MageMinds