I understand that Firewire 400/800 and Thunderbolt have DMA enabled, and a malicious hardware device can easily read and manipulate system memory at will. If I disable the software drivers for these devices, would that prevent such reading/writing? Or is the only way to protect against DMA by desoldering the controller or injecting epoxy in the ports?
Disable both interfaces in BIOS and then password protect the BIOS configuration. Additionally, remove the drivers/modules from kernel for both. Also mind, that DMA attack is possible through ExpressCard interface that many notebooks have. One of the more drastic measures is to fill the ports with silicon gel (or similar) or unsolder them (greater chance to damage something if you are not experienced).
To avoid DMA attacks on Mac through FireWire or Thunderbolt, you just need to setup an EFI password. This will disable raw DMA access (confirmed by Apple Tech Support).