Does anyone know of any research into compartmentalized network protocols? Specifically I'm wondering about protocols where components co-operate to acheive some goal but don't know enough to compromise the entire network. I'm sure the botnet guys have done a lot of work on this but I'm wondering there are any good references in the open literature.
Not sure about network protocols, but, the systems research version of this is called multi-level secure systems. You might want to start looking there.