Yes. It is possible to rename or delete MDM repositories however it is performed through the Atom Management console with AtomSphere. MDM repositories are essentially cloud Atoms attached to the hosted MDM cloud.
Switch to AtomSphere > Atom Management > select MDM cloud instance > Settings & Configuration > Account Properties.
You can also delete the repository with Delete Atom. Note that as a protection it will not let you delete the repository if there are still models deployed. Undeploy the models from MDM first and then delete the repository.