What version of CM are you using? We've also made some improvements in 5.5
that should help with this, and more is on the way.

Onto your question of CLI, you can certainly utilise the API to manage your
replications just as you would on the UI. Look for the "/replications/"
endpoints in the API docs at
http://cloudera.github.io/cm_api/apidocs/v11/index.html (more on API and
Java+Python bindings on http://cloudera.github.io/cm_api/).