Alicia's first impressions of John, before his diagnosis, are generally positive; she views some of his eccentric behaviors as charming and unique, and she doesn't seem to mind that he seems to live by his own set of rules. She marries John because she loves him, and she probably had rather high expectations for their life together as John's talents were already obvious to her and to his academic community.
When John starts to unravel, Alicia may have experienced a number of difficult emotions. She may have experienced fear, as John's erratic behaviors were beginning to seem unpredictable and almost dangerous, and she may have also experienced self-doubt. Alicia may have questioned her own sanity: how could she have missed such clear signs of shaky mental health in the man she loves? Their relationship is changing as Alicia learns the truth about her husband, and she grows a little distant from John as she tries to figure out what is going on.
After John's diagnosis, Alicia is no longer a young wife with a bright married future ahead and she accepts with some trepidation her new role as primary caregiver of her husband. They have a baby at this point, and she must also worry about looking after their young son and to keep him safe from his father who does not mean to be neglectful of the baby when the voices in his head distract him. Alicia is likely very disappointed that her marriage and her life have taken this turn, but she stands by John and she copes with her own disillusionment and moments of depression.
So even though their relationship is tested by John's illness, Alicia's commitment to him and to their marriage helps him to regain his health and autonomy. By the end of the film, their marriage appears steady and strong, and John honors Alicia by giving her all the credit for his success, which is as loving and heartfelt a message as he could give her.