Setting an integrated southbridge device (like SATA or USB2.0) to "off" in Config.lb should cause the PCI device not to respond to configuration requests. The code that takes care of this for the Intel 3100 is in src/southbridge/intel/i3100/i3100.c. Unfortunately I copied the esb6300 implementation without noticing that it makes no sense at all on the Intel 3100. The attached patch implements this properly for the Intel 3100.
--Ed