Lot of text but there are some holes. I wouldn't say the Witness is fulfilling the Winnowers will since there is no proof of this. If anything he just a powerful darkness wielder, and the Winnower is just going about its business. Just like how guardians claim to serve the traveler but have no idea what it's will is. Also the Witness wants to destroy everything to reveal the final shap, but the Winnower just wants to continue the flower game, ergo the Witness is following his own will not the Winnowers, as under the flower game rules any group that forms communities survives. I do think the whole purpose and grand story arc is heading to harmony. However the Winnower isn't evil its just trying to play the game and complete the pattern. After all the Winnower represents death and decay which is a vital part to the life cycle. Otherwise we would run out of resources to support all the living creatures and new creatures would never get a chance to flourish. If anything the Traveler/gardener is more evil since it wants everything to live and is willing to abandon its responsibilities to try and see this goal to fruition. So without the gardener present to play the game, everything falls out of balance. I mean it's literally breaking the laws of nature by resurrecting the dead. If I had to guess I'd say the saga will end with us killing both or sending the gardener back to the garden with the Winnower.