RTD subverted the idea of the Doctor as God, not supported it.
The imagery of the Doctor as an all powerful deity is constantly juxtaposed with him being unable to prevent death despite his most desperate efforts. Astrid’s resurrection is impossible and the notion of choosing who should die deemed monstrous, and the Master rejects the Doctor’s salvation to spite him. When he does eventually snap and and become the Time Lord Victorious, he is undermined by the actions of the very woman he saved.