[Core] Fix inventory unit orphan removement

This fix https://github.com/Sylius/Sylius/pull/1174 does not help if we remove unnecessary inventory units
You could see why, here https://github.com/doctrine/doctrine2/blob/master/lib/Doctrine/ORM/UnitOfWork.php#L332-L338
UnitOfWork marks orphan entities to be removed before "onFlush" event. 
And after https://github.com/Sylius/Sylius/blob/master/src/Sylius/Bundle/CoreBundle/EventListener/OrderItemInventoryListener.php#L62 we need to re-commit entity to remove orphans.