You can definitely rebuild the newest stable firmware, and flash it. That would have EEPROM enabled and you can change that setting. Or you can wait until another stable version comes out.
Anttix has been working on configuring github to automatically build our Marlin configurations. When that is finished, we would have a .hex made by githin, and you could install avrdude on the pi, and an octoprint plugin, and flash the board with the .hex over the web ui… But there are several pieces there that need to get in place before that will work.