You can disable an ethernet port by unlocking the bios advanced menu and then disabling the PCIe root port for that ethernet port. I can provide more details when I have the board in front of me.
I have the same server (FireEYE 5400-EX). I was able to get past the bios password by flashing the Supermicro bios from a DOS USB drive. Perhaps you can do the same via PXE. After flashing the BIOS I powered off the server, unplug the power, removed CMOS battery, shorted JBT1, then put...
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