I read the thanking of God in a few ways. I think it's helpful to look at the final four stanzas one by one:
So still he was that the birds flew round /
The grey of his head without
Leading up to the end of the poem, the Seed-Merchant is at peace within the natural world, exemplified by his stillness. I see a contrast here between the machination of warfare, especially chemical (viz. "unnatural") warfare, and the serenity of the natural world. Nature provides a place of solace in the midst of the violent, destructive consequences of war.
Careless and tranquil in the air, /
As if naught human were standing
The stillness of the man affects the natural world: the birds are "[c]areless and tranquil." There is no divide between man and nature. Instead, it is as if no human were even there. If this were the throes of war, the birds would certainly not feel that tranquility. Given the spiritual implications of the final lines, I cannot help but imagine St. Francis of Assisi preaching to the birds (source).
Oh, never a soul could understand / Why he looked at the earth, and the
seed in his hand, /
The idea that "never a soul could understand" the Seed-Merchant's actions has to do with the idea that his act of faith, or piety even, goes beyond the logic and the rational. In a world torn apart by war, of course this does not make sense. However, I contend that the fault is in the on-looker, not the Seed-Merchant. To him, his actions make perfect sense and culminate in the final lines, but to a world that just fought what was supposed to be the war to end all wars, it does not. It's our souls that are at fault, not the Seed-Merchant's. Indeed, the world is so affected by war that even at the level of individual souls, people cannot recognize simple acts of faith for what they are. The world has been corrupted -- body and soul -- by the violence of war.
As he had never before seen seed or sod: / I heard him murmur: ‘Thank
God, thank God!’
The seed, a metaphor for new life, new beginnings, possibly resurrection, evokes a fresh awareness of the beauty and power of the natural world. The humble seed (possibly an allusion to having faith the size of a mustard seed?) keeps this man going because in it lies the hope of creation. Again, the natural world -- this time a tiny seed -- contrasts with war. Despite all the human-created weapons that seek to wipe out life, the seed exists to create life anew. Compare the seed to artillery: it is almost absurd how such a small thing creates life after such massive forces work to wipe it out. Yet, thankfully, the world can go on, can be re-created, because of something as simple as a seed. The Seed-Merchant knows the promise of life contained within each seed he plants.
And so he thanks God: it is through the seed that the world can continue, that nature can thrive again, that all life does not end because of war. There is suffering and death, but there is also resurrection and new life.