[Core] Fix inventory unit orphan removement

This fix https://github.com/Sylius/Sylius/pull/1174 do not helps 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.