nifr kindly gave me an answer on Github:
https://github.com/KnpLabs/DoctrineBehaviors/issues/294#issuecomment-190310921:
Quick 'n dirty:
$entityManager = $this->getDoctrine()->getManager('default');
$eventManager = $entityManager->getEventManager();
// remove the softdeletable subscriber
$subscriber = $this->get('knp.doctrine_behaviors.softdeletable_subscriber');
$eventManager->removeEventListener($subscriber->getSubscribedEvents(), $subscriber);
// remove entity while the subscriber is removed
$entityManager->remove($entity);
$entityManager->flush();
// add back the subscriber
$eventManager->addEventSubscriber($subscriber);
PROBLEM
This triggers the error "you have requested a non-existent service
", because the service is not public.
To resolve this issue, according to nifr, 2 possible solutions:
1) define your controller itself as a service and inject the subscriber-service explicitly
2) create a factory-service that would return the subscriber service and call that one in your controller