You can get values from form in controller by calling getData():
$form->bind($request); //after this
$data = $form->getData(); //all fields array
$username = $form->get('username')->getData(); // only username field value
$username = $form->get('username')->getViewData();//before mapping/traansformation
So you can encrypt password after checking that form is valid:
$form->bind($request);
if ($form->isValid()
{
$newPassword = $encrypter->encrypt($form->get('password')->getData());
$user->setPassword($newPassword);
}