If you remember the whole incident about her being taken as a child, she is taken in "A Good Man Goes to War" and the next time we see her in the Doctor's timeline is the next episode, "Let's Kill Hitler". Even though she was only an infant at the first point, she met the Doctor for the first time there and the rest of the following events were in order for her.
(Her last meeting with the Doctor, when she "dies", also may not have been the last of her. There are stories about consciences being transferred from memory banks and the like to living bodies, like the Doctor's Daughter who was created from his DNA.)
So it isn't two straight timelines running parallel (one backward, one forward). "People assume that time is a strict progression of cause to effect, but actually, from a non-linear non-subjective viewpoint, it's more like a big bowl of wibbly wobbly timey wimey... stuff." Just remember that what we see onscreen is linear, but the Who-niverse is not.