Sadly Babel is still a work in progress and this functionality is not yet implemented. In fact the design of how this will work is not yet fully worked out. I believe it will work somewhat like this: you will be able to specify a 'default' branch in packages.json file for your package.
Different versions of your package should be git tagged, and in the future you will be able to specify a branch/tag to install when installing a package with babel.
I find that the current design is not yet perfect and that we may need to think about a total overhaul, I am always open to suggestions.