SPOILERS!!! SPOILERS!!!! SPOILERS!!!Well, she did have one more choice - not take either scenario - leave by herself.
Well, yes but keeping her husband would made things a lot easier for her. At least economically speaking. Leaving on her own would still be tragic for a woman like her. Starting a life all over again, on your own, with a baby on the way is not something many women would like to do. Her husband was an pothead and an idiot, but he loved her and she knew he would be there for her and the baby. At least she hoped so. Plus, she already had a job, and a home for the baby so there was no real point in leaving, even if that meant being a doormat. She could always divorce Phil and at least keep her job. I thought the ending was realistic.
I think Justine's problem was that she was bored with her life. Her daily routine bored her to death. That was the reason for her unhappiness. I think the whole movie speaks about boredom. Everyone there seemed bored and sought different ways of entertaiment. Phil and his friend smoked pot; Justine slept with Holden, the girl played by Zooey Deschanel insulted and made fun of the customers, and the guard went to bible study. Perhaps after learning she was pregnant, Justine saw a way out of her boredom, and didn't see the need to leave or change her life entirely by running away (with Holden or on her own).