Well if you disable the SATA ROM, then no oprom loads to handle SATA so the OS won't be able to see those devices....that's expected. It sounds like you're running into a ROM space issue. You have the right idea in trying to turn off items that eat up space that aren't needed...you just picked the wrong one I think
If you're not using any of the blue SATA ports, then you could try to turn off the Marvell controller. Another option would be to disable PXE boot and see if that opens up some additional space for you. Could also disable the 2nd LAN completely if you're not using it in an attempt to save space.