Adaline ran away from Ellis at the end for the same reason she ran away from William. She knows she doesn't age and that is her secret. First, she doesn't want anyone to know and second, what kind of life would it be to watch your spouse, the person you love dearly, fade away with age while you remain static in time. She has already done that with her daughter.
Keep in mind while William did reveal that he knew it was her, Ellis still did not know. Throughout the movie it was clear that Adaline avoided personal relationships, especially love interests. She was falling in love with Ellis and she knew it. When she realized who William was, she was reminded of what would happen and also realized that she was letting herself get too attached to Ellis, thus breaking her own rules.