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Hester chose the name “Pearl” to represent something of great value, namely, the cost of her virtue and place in society (see Matthew 13:46, where the pearl costs everything a person has, but it is worth the great price). Hester is afraid that nothing good can come from her sin, however, and thus she fears that Pearl will in some way be retribution for her sinful passion.
From the text:
Her Pearl--for so had Hester called her; not as a name expressive of her aspect, which had nothing of the calm, white, unimpassioned lustre that would be indicated by the comparison. But she named the infant "Pearl," as being of great price--purchased with all she had--her mother's only treasure!
http://www.gradesaver.com/the-scarlet-letter/study-guide/summary-chapters-5-8; The Scarlet Letter