This isn't about agreeing on everything, or even on anything. It's about not taking their disagreement public. He was elected President, she wasn't.
Not that I really have a problem with her saying whatever she wants, because I'm not the one married to her. I just don't think it's likely that she would have if he didn't agree to it. It's generally considered bad form.
But you know she's going to be asked these types of questions by the press, and she should reply truthfully.
It's bad enough that when she agrees with him, some on the left say she's being the "perfect little wifey".