Recently Jonathan committed a patch to support Entity aliasing.
Patch at first glance looks good, but it has some issues (it double processes the loadedMetadata).
I have fixed this issue by including a new level of configuration. Instead of create a 1 alias => 1 entity hashmap, I added support for namespacing.
The idea is similar to AnnotationReader support recently introduced.
To take advantage of it, simply include the $ormConfig->addEntityNamespace('CMS', 'Doctrine\Tests\ORM\Models');
Then, just do: "SELECT u FROM CMS:CmsUser u"
This is also supported in $em->getReference(), ->getRepository(), etc.
Patch is attached including updated unit test plus another test for getRepository().