I wouldn’t say Emma’s thinking is “flawed,” per se, since she was speaking emotionally as a child who suffered a great deal, and not necessarily as one who could objectively see the bigger picture yet. She’s going to have to process it, talk it through with Snow, and understand that there really was no better choice. The curse was designed to rip apart Snow White’s happiness, and there’s no way that Regina would have allowed Snow to keep her baby or her husband. Emma would have ended up in a foster home and remained a baby all her life, or she would have been killed by the Evil Queen’s guards back in FTL right before the curse hit.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy