I have this scenario:
Answer was less complex than I expected.
It seem to be sufficent call $this->entity_manager->clear();
that will clear this entity map and force it to reload from database into a brand new object!
$this->entity_manager->clear();
$aCopy = $this->entity_manager
->getRepository('MyBundle:A')
->find($a->getId());
$this->logger->debug('Original Obj: '.spl_object_hash($a));
$this->logger->debug('Copied Obj: '.spl_object_hash($aCopy));
this will print
[2013-02-08 12:07:20] app.DEBUG: Original Obj: 000000006523645c000000004b1160d1 [] [] [2013-02-08 12:07:20] app.DEBUG: Copied Obj: 00000000652366e3000000004b1160d1 [] []