I don't think it was a miscalculation. There are people like that. When Skyler met Walt he was in a phase (or spiral) of meek self-flagellation. She got used to that and didn't mind being in charge. When Walt asserts himself, she's shocked and that sudden dynamic shift (along with the stress of the diagnosis and the money problems) makes her lash out. She subconsciously blames Walt and she hates not being in control.
That's not a very nice person, but it's a realistic person. It adds to our sympathy for Walt in the first couple seasons (until he descends into tyrannical mania) which is necessary to get us to see the nuances of each character.
The show doesn't have heroes and villains. It has Walt, who is tactical and assertive, but who uses his gifts to hurt people. There's Jesse, who is unambitious and apathetic to the damage his drug-dealing causes; as the show goes on, however, he develops more of a conscious and tries to escape. Skyler, Hank, Marie - all the characters are good and bad. Marie supports Walt (the talking pillow) but is a kleptomaniac. Hank serves the law and justice, and is as loyal as you could ever want, but is also a total dudebro and often bullies people (sometimes unintentionally).
In summary: I don't think it's a miscalculation. Likeable or hateable, Skyler is just part of that roster of grey morality.
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