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When the Rev. Dr. Amy K. Butler was hired to lead Riverside Church in Manhattan in 2014, she was hailed as a rising star, the first woman to join a distinguished line of pastors at one of the pre-eminent progressive Protestant congregations in the United States.

This month, Riverside’s governing council refused to renew Dr. Butler’s contract, shocking the 1,750-member congregation. The decision followed a series of charges and countercharges over sexual harassment, sexual mores, culture and hypocrisy in a church where past leaders had marched for civil rights with the Rev. Dr. Martin Luther King Jr.

Dr. Butler’s supporters said she lost her job because she had spoken out about sexual harassment and she had complained in particular about an incident in which a former member of the church’s governing council left a bottle of wine and a T-shirt on her desk, both with labels that read “Sweet Bitch.”

They said she had pursued better treatment for women and minorities, with the aim of fixing a difficult environment that had led some church employees to complain and even quit. Her persistence strained an increasingly fractured relationship between her and the church’s lay leaders, her supporters said.