Whether or not it makes sense to invest time in, is always a question. To me, LinuxMCE is a learning platform.
It is a two way process. Luckily, everything that you need to do on the core, you should be able to do from the joggler via SSH. I would envision something like this:
On the core, run a script that creates an USB stick capable of booting on the joggler and flashing the Joggler with needed stuff. Add the private key from the core to the USB stick to allow the joggler booted from the USB stick to execute commands on the core.
Joggler boots with USB stick, startup scripts on the USB stick flash the joggler, connect to the core, does the magic on the core, prompt user to reboot and unplug the usb stick, and Voila! - perfect