Why can't Castiel hurt Manhattan?
Manhattan may be a "God" in comparison to regular humans, but you have to remember while he's quite powerful he's never shown immense levels of power in comparsion to other beings I thinik Castiel can kill him.
Castiel an angel is capable of soul rape, he can just convert Manhattan's soul into energy, and wipe him out, and hell wipe out NYC and the Watchmen, or cause him immense pain via the soulreading technique.