I'm not sure which is faster, the rsync method or the direct-disk-copy method.
I've never measured disk-to-disk bandwidth on an Empeg, but memory-to-disk bandwidth is about 6Mbytes/sec (which probably saturated the head rate of the winchester), so with a bit of luck disk-to-disk should be at least 3Mbytes/sec, or far faster than USB or rsync. (Unless, of course, you're using rsync to make minor updates to an existing duplicate copy.)
The only faster way would be to plug both disks into a Linux PC, which will certainly be able to saturate head rate on both disks for a throughput of 6Mbytes/sec -- perhaps more with modern disks.
Peter