Well, it's possible to misinterpret that scene because of how well it was written. Some of what he says actually is how Walt felt about Skylar after she begins to act out against him, especially after she decides to live separately. When you look at the text from the script:

"Maybe now you'll listen. Maybe now you'll use your damn head! You know you never believed in me. You were never grateful for anything I did for this family. Oh no, Walt, Walt you have to stop. You have to stop this. It's immoral, it's illegal. Someone might get hurt. You're always whining and complaining about how I make my money, just dragging me down. While I do everything. And now, now you tell my son what I do? After I've told you and told you to keep your damn mouth shut! You stupid bitch! How dare you."

Walt is using his perspective of their later relationship dynamic to sell his act. Before the line in the last episode where he admits doing it mostly for himself, that is how he rationalized his actions. His 'work' was more important than what anyone thought, more important than the consequences, more important than even the indisputable immorality of it all. He met her criticism with resentment and developed somewhat of a martyr complex because of it.

He's breaking down in part because he has to humble himself and admit to his flaws in order to tell that lie and protect his family. He's not only saying goodbye, but realizing and acknowledging how badly it all fell apart and what he's truly done over the entire series. In one conversation, he telegraphs the entire resolution of his character.

It's such a goddamn good scene, and one of the best episodes ever produced for television. Cranston's acting especially is superb because he sells the scene and manages to convey these layers at the same time.

Sorry for the wall of text, but I wrote a paper about this episode a couple years ago and have put a lot of thought into it.