I really enjoyed these AU glimpses. I think you're right; his other companions would have stood up to him, and that's because the Doctor helped them build up the self-respect to do that. He never gave Martha that.
Author's Response: I think Martha DID eventually get that, but much later than Human Nature/Family of Blood, and it had little to do with anything the Doctor did for her directly. Martha sort of just got fed up with the whole thing and took a stand all on her own, from what I can see.