I was on a talk at weardevelopers.com from the CTO of BWin and they actually version the configs in their own config service.
they even have a json key { app: 'name', version: 'v3' } so maybe just using a versionservice with a websocket where you can push such info? a classic bus distribution so to say to update and bootstrap the services in runtime?
those would be my thoughts. you could just basically have a 'dumb' http server that basically just returns a static json and has only 1 endpoint.
which you pass as an CLI or ENV parameter.
you could also just create seperate isolated configs and deploy them via puppet or ansible or fabric.