Despite the fact that some basic facts of life are different in The City of Ember—no sunlight, no sky, no animals—families remain an important part of people's lives. The key difference is that families seem smaller, more broken, since folks don't seem to live very long. However small and fractured families are in Ember, though, there's still a lot of love: think of how strongly Lina loves and wants to protect Poppy, and how loving Doon's father is in raising and encouraging him. Maybe their precarious existence makes these families even closer.
Mrs. Murdo should have been taking care of Lina and Poppy all along because families built on love will last longer than families based on blood.
It was more selfish of Lina to take Poppy with her on the boat than to leave her behind in Ember.