I found all of references to corruption in the church disturbing.
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Although this novel is actually based on the life of Jean-Baptiste Lamy; it also takes the time to partially chronicle the construction of the Cathedral Basilica of St. Francis of Assisi. Actual historical figures such as Popé, the Penitentes, Pope Gregory XVI, John C. Frémont, Kit Carson, and Saint Paul are also mentioned in the novel, as well as the War in Italy, Bosque Redondo, and the Pike's Peak Gold Rush.
Cather does a remarkable job with keeping it all real, and unfortunately much of what you found disturbing is very real. The two French priests sent to take the place of the residing clergy found an inordinate amount of greed, avarice and gluttony amongst the clergy, but they also found many clergymen living simple lives and working in the service of God in the Native American communities.
Historically, the Church, has been robbed and taken advantage of by self serving priests and even bishops, popes and cardinals; that's just a fact. It doesn't mean that the Vatican was aware of it or that is condoned their behavior, but it doesn't mean that they didn't either. The Catholic Church will always come under fire for those who served themselves before God, but these people DO NOT represent the whole. Nonetheless, their actions do make for great novels, and there have been many.