I'm not totally sure I follow what you are saying, but I think that with the new passport for your wife that your last name has been appended. I think if your wife also carries her old passport with her, that would mitigate any questions raised. It seems that your concern is more with JLA than TAM. You wife is Brasilian, once in Brasil, I don't think she will have any problem. Maybe others have had an experience that matches yours and can provide additional insights.