One popular way of doing it would be to deploy each application: streamloader, mutator and repeater as a GKE Deployment. For the HOCON and Iglu resolver JSON, you can use another GKE resource, called ConfigMap.
In the Deployment, you specify the name and version of the container to use, as well as the arguments to be passed to the container. You would store the configuration as ConfigMap objects, which you then pass on to the Deployments via the args.