Stein resigned because of the partisan nature of Carter's book. In the critique he effectively explains why he resigned.
While Carter says that he wrote the book to educate and provoke debate, the narrative aims its attack toward Israel, Israeli politicians, and Israel's supporters. It contains egregious errors of both commission and omission. To suit his desired ends, he manipulates information, redefines facts, and exaggerates conclusions. Falsehoods, when repeated and backed by the prestige of Carter's credentials, can comprise an erroneous baseline for shaping and reinforcing attitudes and policymaking. Rather than bring peace, they can further fuel hostilities, encourage retrenchment, and hamper peacemaking.
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