The DMA mentioned in the article was internal to the drive, between the hardware interfaces and it's internal cache. The drive did not have DMA access to system memory.
Even though it wasn't discussed in the article, I think firewire and thunderbolt external drives DO have direct DMA access to system memory. Google for SBP-2 and DMA, and a bunch of articles about protecting against firewire attacks against full-disk-encryption (among other things) appear.
I know you're right on FW. I believe DMA was designed in because they recognized that the CPUs of the time weren't powerful enough to move uncompressed full-resolution video from around. I don't know about Thunderbolt, but I'd expect you're right.
IIRC DMA was designed to allow peripherals (floppy drives, parallell ports, etc.) to move data from their input lines to regular memory without having to bother the CPU. Uncompressed, full resolution video wasn't too much of a real concern back in the days of the 80286 :-)
