Without taking a long gander at it, it should be possible. Almost all of the RAID function in Linux is within the kernel, if I understand it all correctly. And Hijack is just a replacement kernel, so we've got that going. There was RAID support, includeing RAID 1 (AKA mirroring) available in Linux 2.2 kernels, which is what the empeg runs.
The only problems I can see are getting the utility programs to run, which probably wouldn't be hard, and making sure that the correct devices get mounted. That is, I believe that the player binary mounts /dev/hda4 and /dev/hdc4 manually, so you'd have to change those devices to point to the metadevice instead of the real hard drive. The problem is that it might check the device numbers and screwup somehow if the devices don't point to the right things. Honestly, I doubt that would be a problem, either, as I feel confident in saying that it doesn't do that.
I'd work on this for you, as it would be pretty cool and not take too awfully long, but I only have one hard drive in my empeg right now. If you want to send me another, I'd be happy to work on it.