I didn't get the impression Sam was a negligent mother. I did get the impression the producers didn't want to pay her actress every time they wanted a cute kid in their story.
There is all this time Naomi is just wandering around the ship. Sam probably has an 8 hour duty shift, and she can't lock Naomi in her room all that time, especially since she knows every single person on the ship will look out for her.
I liked the ending of that episode. I didn't see it as coming off as Star Trek preachiness, I saw it as a good way to represent the world's pluralism.