No, the River seen in "The Name of the Doctor" is from after the events of "Silence in the Library." You are correct when you say that we're seeing her "saved" mind that is stored on the Library's database, and this is possible because she was part a psychic conference call that transcended time between herself, Vastra, Jenny, Strax, and Clara. No physical body was required.
Her dialogue is fully indicative of this, as she talks about the Doctor "leaving her like a book on a shelf" and already knows his name, which she had learned by the time that she died in the Library. The Doctor likewise states that she is an "echo" like Clara and that she "should have faded by now." Vastra also appears to be familiar with this fact, as she asks River if the Doctor ever contacted her after leaving her, and we know from "A Good Man Goes to War" that the Doctor has told Vastra a lot about his adventures. She is also using the white dress that she was wearing in the final shots of "Forest of the Dead".
Just to further the point, an issue of Doctor Who Magazine stated that she was "River Song - back from the Library."
Remember that River's appearances are not always sequential. That's how we could see a River who was just about to earn her pardon all the way back in Series 5 ("The Time of Angels"), and then see one who has just been pardoned in Series 7 ("The Angels Take Manhattan"), or how we could see a River who had "just climbed out of the Byzantium" ("Flesh and Stone") at the end of "The Wedding of River Song". Accordingly, the River in "The Name of the Doctor" needn't have just come from the events of "The Angels Take Manhattan" and can instead be from other points in her timeline (this one just happened to be post-mortem, because the mind that partook in the conference call had been saved in the Library's database and was the one that got contacted for the call).
