Memory slot direction doesn't seem that important. At least, I've got a desktop board in a rack that seems happy enough. Or is there something other than memory direction that puts you off, ipmi perhaps?
If you put it in a 1U case I would be very surprised if it didn't matter - I'm doing that with a very low power platform and the clearance between the memory and the case only leaves a 2-3 mm gap, which I doubt would permit sufficient airflow for a normal passive CPU heatsink with a normal CPU power.