Ah, OK, I must've mis-remembered a line of dialogue, about "my sister" somewhere along the way that led me to believe she was the Commander, or at least another sister
(For example, maybe The Doctor went back and saved her (Or he had a profound impact on her, that allowed her to save herself), and she became a force of good in the Universe)
In AGMGTW it is said that the Doctor prevented Vastra from murdering innocent people in response to the death of "her sisters" as a result of the construction of the London Underground. Clearly a different incident.