Ela não fez, o próprio médico fez. Ele na verdade (tacitamente) admite isso no episódio mencionado na pergunta:
River: Turns out the person I killed never existed in the first place. Apparently, there's no record of him. It's almost as if someone's gone around deleting himself from every database in the universe.
Doctor: You said I got too big.
Doctor Who Series 7 Episode 5: "The Angels Take Manhattan"
E é trazido de novo em "Nightmare in Silver":
Cyber-Planner: Doctor... why is there no record of you anywhere in the databanks of the Cyberiad? Oh. You're good. You've been eliminating yourself from history.
Doctor Who Series 7 Episode 12: "Nightmare in Silver"
Tudo o que Oswin fez foi apagá-lo da Path Web, a mente de Dalek; isso é algo que o próprio médico não poderia fazer:
Owsin: The Daleks, they have a hive mind. Well, they don't, they have a sort of telepathic web.
Doctor: The Path Web, yes.
Oswin: I hacked into it, did a mass delete on all the information connected with the Doctor.
[...]
Dotor: I've tried hacking into the path web. Even I couldn't do it.
Doctor Who Series 7 Episode 1: "Asylum of the Daleks"