It seems like there is no solution to manually trigger the dispatch of the confirmation email. It's only triggered in combination with the registration form. What I ended up doing is to fake a form and the dispatch of it to trigger the event listener responsible for the dispatch of the email.
//use FOS\UserBundle\FOSUserEvents;
//use FOS\UserBundle\Event\FormEvent;
$formFactory = $this->get('fos_user.registration.form.factory');
$form = $formFactory->createForm();
$form->setData($user); // created user object
$event = new FormEvent($form, $request); // request of the Controller
$dispatcher = $this->get('event_dispatcher');
$dispatcher->dispatch(FOSUserEvents::REGISTRATION_SUCCESS, $event);
Not really a clean solution, but the only one I could come up with, as the FOSUserBundle doesn't seem to offer any kind of API for it.