After discussions with the Mongo PECL maintainers this functionality has not reached the pecl level yet. However there is still a silver lining.
Doctrine\MongoDb\Database has a command() method which allows you to do something similar to:
$mdb = ''; // Really it would be a mongo adapter
$db = new \Doctrine\MongoDB\Database(
$mdb, // Our \Doctrine\MongoDB\Connection
$mdb->selectDatabase('admin')->getMongoDB(),
new \Doctrine\Common\EventManager()
);
$success = $db->command(array('renameCollection' => 'foo', 'to' => 'bar'));