The sudden reintroduction of the baby story-line just follows that life happens even while trying to save the world. That's been part of the point of Alex's story, that she can be a mother as well as a savior without having to sacrifice one over the other. And since life surprises, then having it suddenly pop up shouldn't fit into an overall plan, it should surprise.
As for a patient/therapist dynamic, I was just seeing it as Kelly being a friend to her brother's friend. She is a therapist, but it didn't feel any different than when Alex would support Kara or vice-versa. Plus, she was using her own experiences to personalize with Alex, which again, they've all done before.