This is quite possibly my favorite Pixane moment in the show, and for multiple reasons.
1- This is one of the first times P.I.X.A.L. gets to show genuine frustration. She does get to show a bit of annoyance in Season 7, but without the Samurai X reveal, we don't really see it developed. Here, P.I.X.A.L.'s not only frustrated, but she gets to work through it too.
2- Zane is such a sweetie. He listens to P.I.X.A.L., he reminds her that her value doesn't come from her usefulness, he supports her decision, and he gives her such a pure little compliment in the process... their dynamic is so heartwarming, and I'm so happy P.I.X.A.L. is out of Zane's head because now they can legitimately interact again.
3- P.I.X.A.L. is still frustrated at the end of the scene. Though she was able to open up about her feelings, it still didn't solve the actual problem. But P.I.X.A.L.'s voice doesn't have quite the same edge to it. It feels like she and Zane are actually working together, and the pressure to excel on her own is no longer weighing her down.
On a slightly different note: I don't think P.I.X.A.L. living in the computer is an inherently bad thing. No matter what, it should always be her choice, and if she wanted to live in Zane's head, that's totally awesome too. Maybe she even enjoyed that for a while, and over time changed her mind. However, her personality is already so much clearer in this little conversation, as compared to the few glimpses we get in say, Possession, where throughout the entire season she is the equivalent of Google maps. It's obvious that she becomes more alive with a body of her own.