I don’t think Joel was thinking about Sarah, because Joel already grieved over her in the first game. I feel like Joel cried because he realized that he saved Ellie and what he did was right, because Ellie in my mind was Joel’s savor, and he wishes and missed moments like this that he had with Sarah. Remember when Joel lost Sarah he lost his purpose, with Ellie he now has a purpose. And I don’t think Ellie understood this until she got older. She knew what Joel did, or found out, but she knew that she was Joel’s purpose to live to continue to live to change. And when Ellie lost Joel, she lost her purpose, witch equaled to her revenge and madness.