I don't think we'll be able to support a Command line interface due to the nature of unity, unfortunately. It will require basic 3d graphics acceleration and visuals. I imagine that the requirements will be low enough to work over vnc, but I'm not positive on that. There's not a way for us to make the game run outside of unity without coding two versions of the entire thing, which would be enormously increasing the amount of work to maintain and extend the game on an ongoing basis, making it something we can't really consider. That pretty much kills the CLI option unless unity randomly adds that as a feature someday, but given their focus I don't know why they would.
THAT said, being able to configure the server via config files is a definite possibility for a bit down the line. So, thinkIng about it, you might be able to run it in a CLI interface as long as the box supports wine and all that, and just not directly interact with it once it is running, just killing it and restarting it if you need to change the config files. I'm not 100% sure that would work on your specific box, but it sounds plausible at the very least.