In this particular stanza the speaker is contemplating what will happen at the hour of our death. He is waiting for some kind of sign that the end is nigh, something more biblical, more apocalyptic than the fires that rage in London after another night of German bombing. Hence his refusal to mourn the death of the child.
One such sign will be the return of humankind to the "Zion of the water bead" and the "synagogue of the ear of corn." In these lines, Thomas is endowing certain features of the natural world with deep religious significance, drawing on ancient words associated with places of worship—"Zion" and "synagogue."
Death is presented, therefore, as a return to the nature from which we came. We all come from nature, and it is to nature that we will return at the hour of our death. It is only when the speaker has conceived of the death of the eponymous child in this way that he is finally able to mourn. For now he is in a position to recognize that the child, in death, is more a part of the natural world, and therefore more alive, than she ever was during her short time upon this earth.