Starting from the 1.8 version of DoctrineBundle, you can extend your class using Doctrine\Bundle\DoctrineBundle\Repository\ServiceEntityRepository instead of Doctrine\ORM\EntityRepository. The result will be the same, but this does support the autowire.
Example:
use App\Entity\Activation;
use Doctrine\Bundle\DoctrineBundle\Repository\ServiceEntityRepository;
use Doctrine\Common\Persistence\ManagerRegistry;
class ActivationRepository extends ServiceEntityRepository
{
public function __construct(ManagerRegistry $registry)
{
parent::__construct($registry, Activation::class);
}
// ...
}