Exactly what I thought Andrew. But the boot process didn't agree. However I've gotten further.
1. Download from Realtek source for r8168 and compile to r8168.ko
2. Rename r8169.ko to r8169.ko.old to get it out of the way
3. Add a line with r8168 into /etc/initramfs-tools-interactor/modules
4. Ran Diskless_BuildDefaultImage.sh to get new default initrd for tftboot
5. Reboot MD - and a new diskless media director is created, 96 in this case (yay!)
Then when the brand new MD is rebooted, get hit by the same r8169 showstopper. So I dig into 96/etc/initramfs-tools/modules and add line with r8168.
Do step 2 in 96/lib/modules/2.6.22-14-generic/kernel/drivers/net/
Next utter the following incantation
mkinitramfs -o initrd.img-`uname -r` `uname -r`
With fingers crossed, reboot
Success? No, greeted by ipconfig: eth0: SIOCGIFINDEX: No such device
I was so close....