It is possible to define your own HTTP handler and inject it before Meteor’s default handlers. It is even possible to reuse Meteor’s authentication tokens from one such custom handler.
Are similar things possible with websockets?
Just to clarify: do you want to hook into the default websocket implementation with your custom messaging system (outside of the DDP protocol) or do you want to run an entire second websocket server in parallel to Meteor’s default one?
Either would work I guess.