"I take no stances on theology, Erasmus," said the doctor. "I am a scientist. But is it not said that we are his instruments? If that is the case, then God brought you to her and directed you hence to my door." (1.14)
Dr. Warthrop clearly doesn't put much stock in religion, but he's at least respectful of the fact that other people do. Not everyone is so open-minded.
I daresay your average adult would have fled the room in horror, run screaming up the stairs and out of the house, for what lay within that burlap cocoon laid shame to all the platitudes and promises from a thousand pulpits upon the nature of a just and loving God, of a balanced and kind universe, and the dignity of man. A crime, the old grave-robber had called it. Indeed there seemed no better word for it… (1.72)
It's actually pretty common for people to question the existence of God when they're confronted with something truly terrible. How could God have created Anthropophagus and then allowed them to commit all of their atrocities if he is, as the Bible says, loving and just?
"I mean no offense, Warthrop. My area of expertise is held in no greater regard than yours. I do not mean to mock or ridicule your life's work, for in one way at least it mimics my own: We have dedicated our lives to the pursuit of phantoms. The difference is the nature of those phantoms. Mine exist between other men's ears; yours live solely between your own." (6.82)
At the end of the book we learn that Dr. Starr has known about the Anthropophagi for over two decades (he was complicit in their feeding, after all), so how can he say that the monsters Dr. Warthrop chases are purely in his imagination? Hasn't he had ample proof that such things exist?
The doctor said nothing. In a slow circle he turned, hands upon hips, pirouetting to survey the carnage, his expression at once one of fascination and detachment, marveling at the sheer savageness of the attack yet removed from its arrant horror, heart divorced from mind, emotions from intellect, the quint-essential scientist, set apart from the very race to which he belonged. (8.48)
Why do you think they say that in order to be the "quintessential scientist" you need to be totally removed from what you're studying? How would being emotionally involved affect the ability to be scientifically apt?
"Perhaps you were spared for a reason, Malachi," the constable said. "Have you thought of that? All things do happen for a reason… Is this not the foundation of our faith? You are here—all of us—because we are but part of a plan prepared before the foundations of the earth. It is our humble duty to discern our role in that plan. I do not pretend to know what mine or anyone's might be, but it could be you were spared so no more innocent lives might be lost." (8.134)
Believing that your life is all part of a grander plan can be a small comfort in hard moments like this one. If it all happened for a purpose, and not because it was random awfulness, then maybe something good could come out of all of the pain.
With a snort the doctor abandoned any pretense of compassion and spoke harshly to the tormented boy. "Your self-pity mocks your faith, Malachi Stinnet. And every minute you wallow in it is a minute lost. The greatest minds of medieval Europe argued how many angels could dance upon the head of a pin, while the plague took the lives of twenty million. Now is not the time to indulge in esoteric debate upon the whimsy of the gods!" (8.137)
Leave it to Dr. Warthrop to take the small comfort Constable Morgan was trying to offer and slam it in Malachi's face. He's doing this because he thinks the events are comparable: Instead of wallowing in self-pity (which in his analogy is as useless as arguing about the physical mass of an angel), Malachi needs to tell Warthrop what he saw in order to help combat the Anthropophagi (who are like the plague). Subtle.
Through gritted teeth he growled, "I know what you're thinking, Will Henry, but even the tenets of the victims' faith hold a mistake to be no sin. A miscalculation is not negligence, nor prudence a crime. I am a scientist. I base my action or inaction upon probability and evidence. There is a reason we call science a discipline! Inferior minds bolt or build pyres to roast the witches in their midst! It is a false argument to assert that simply because we do not see fairies dancing upon the lawn proves naught as to their existence. Evidence begets theory, and theory evolves as new evidence emerges. Three thousand years of research, direct eyewitness accounts, serious scientific inquiry—was I to abandon all of it upon the doorstep of speculation and doubt? In all crises are we to demand reason's abdication or, worse, champion the coup of our baser instincts? Are we men, or anxious gazelles? An impartial examination of the facts would lead any reasonable man to conclude that I am blameless, that I reacted with prudence and forbearance in the case, and indeed a lesser man might have squandered his energies pursuing those fairies on the lawn, which no one can see!" (8.224)
Dr. Warthrop worships upon the altar of science. He believes in no higher calling, and that strict adherence to scientific tenets is all that he needs to live a righteous life. In this way, he is trying to justify the guilt that he's feeling over the deaths of the Stinnets. He merely followed scientific precedent; it can't be his fault that he didn't alert anyone else to the Anthropophagi's presence.
"It was Elizabeth," he said. "My dream. We were in this dark place, and I was searching for her. She called my name, again and again, but I could not find her. I searched, but I could not find her."
"She is in a better place now, Malachi," I offered.
"I want to believe that, Will."
"My parents are there too. And one day I'll see them again."
"But why do you believe that? Why do we believe such things? Because we want to?"
"I don't know," I answered honestly. "I believe because I must." (10.205-210)
Malachi is going through some pretty normal grieving processes. He is questioning his faith after a terrible ordeal and wants Will Henry to reassure him. Will Henry, doing his best, admits that he has to believe in such things because otherwise the pain of losing his loved ones would be too much to bear. That's a good enough reason for anyone.
"I don't know what you mean."
"Oh, you must. That euphoric moment when you hold their life here." He held up his hand, palm facing us. "And now you are the captain of their destiny, not some ineffable, invisible fairy-tale being. No? Well, I suppose intent has everything to do with it. The will must be there. You didn't really intend to blow his brains out." (11.60-61)
It's not that surprising to see that this is what Dr. Kearns thinks about religion. Religion wouldn't serve the same purpose for someone like him—he needs to be his own moral authority in order to justify many of his sketchier actions.
My fortitude gave way. I was but a boy, you'll recall; a boy who had been in his share of tight spots and dire straits, to be sure, a boy who had seen things that would make a grown man blanch, but still a boy, still but a child. I slid down the wall and rested my forehead against my upraised knees. I closed my eyes and prayed. My father had not been a particularly religious man; aspects of the divine he had entrusted to my mother's care. She had prayed with me every night and had taken me to church every Sunday, to instill a bit of piety in me, but I had inherited my father's indifference to religion and had gone through the motions of devotion without much conviction. A prayer was mere words repeated by rote. When I arrived at the doctor's house, of course, all churchgoing and prayer had come to an abrupt halt, and I did not pine over the loss. But now I prayed. I prayed until I ran out of words, and then I prayed with my entire being, a prayer not composed of words but out of the profound, wordless longing of my soul. (12.202)
Sometimes in moments of desperation things that were instilled in you at a very young age can emerge again. Will Henry isn't particularly religious but he remembers how to pray, and in this circumstance it is just what he needs.