Yes the little girl was in fact Amy and Rorys daughter Melody . Silence stole her as a baby but she escaped. Later as an adult she finds her parents changes her name to keep it a secret untill the right time.
In fact, Melody's name is a stable time loop, as Melody Pond was named after Mels, who would later regenerate into River Song, who later revealed herself to be Melody.
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Melody/River