I partially answered my question. The object returned from a resource method is attached to the MessageContext object's responseEntity property. I assume messageContext.setResponseEntity() is invoked by org.apache.wink.server.handlers.RequestHandler.InvokeMethodHandler but haven't verified this.
I still have to figure out why, when my byte[] is serialized into json that it is not assuming the UTF-8 encoding (and subsequently mangling my special characters)