Disclaimer: I don't own Once Upon A Time and never will. No copyright infringement intended.
When Emma Swan first met Mary Margaret Blanchard, she had no idea how close she'd actually become with her son's teacher. Emma still doesn't understand why she took her in when she had nowhere else to go, but she isn't complaining.
Somewhere along the line, she and Mary became went from roommates and friends to family. And deep down, Emma meant when she told Jefferson – She does wish a little bit that Henry's book was right, that Mary is her mother. (Then again, it means that ass David is her father, and she isn't sure what to do with that information.)
She doesn't mention it to anyone, but Emma sometimes dreams about growing up with Mary and David (or Snow White and Prince Charming) as her parents. They're completely random, and she blames it on Henry getting to her. That's all it is. She won't be drawn in by her son's fantasies and his book of fairy tales no matter how much she wants to be. Emma is a rational thinker and she'll stay that way.
But after being kidnapped by Jefferson, something shifts. Emma's denial is chipped away for once.
And the curse cracks just a little bit more.