I'm still having a lot of thoughts about Wake up Dead Man, and most of them fall under the heading of "man, that movie was really over-sold to me as a refreshingly nuanced look at people of faith." I've been in the movie's Tumblr tag, and I'm realizing now that a lot of those kinds of comments are coming from atheists or people who have been harmed by the Church. And it's no surprise because this movie is specifically tailored to atheists and people who have been harmed by the Church.
It's sure not tailored to Catholics. Every Catholic or ex-Catholic in the comments is asking where Mary is, and some of them are answering that question for themselves, but they're doing so without any help from Rian Johnson's script.
More importantly, though, the overall portrayal of believers is strikingly negative. The conversation Benoit Blanc and Father Jud have in which they lay out their opposing views on faith early in their partnership is superficially about them respectfully agreeing to disagree, but it is Benoit's view that is born out in the behavior we see from almost every Catholic character who isn't Jud. Father Wicks drives out a single mother and a gay couple with his judgmental sermons. Misogyny is pervasive through his church's history, both gleefully enacted by the men and internalized by the women. Meanwhile, Jud's kindness, compassion, and forgiveness--pretty standard values within Catholicism and other forms of Christianity--make him such an aberration that most of his congregation will not even speak to him for most of the movie. Granted, they are in Wick's thrall, but even characters within the Church who are not fare little better. The cardinal (I think), Jeffrey Wright's character, knows that Wicks is bad news, but his solution is to send a baby priest to go deal with him by himself. The only person who is willing to offer Jud any help is a self-styled "proud heretic."
Jud is a wonderful character and a wonderful example of what a good priest can be. But his first interaction with another Catholic in the movie is when he punches another priest in the face, an action glossed over by his cardinal because that priest was "famously a dick." Apart from that cardinal, the only validation he gets from within his own faith is from a character who spends most of the story despising him, and then only when she's dying in his arms. Benoit, meanwhile, recognizes these qualities in Jud immediately and seems to see them as wholly coincidental to his faith. Jud is the exception that proves the rule.
However, one does not have to go far to find a much more balanced representation of Catholicism. Lisa McGee's How to Get to Heaven from Belfast (also on Netflix) centers on the friendship of four Irish women who went to Catholic school together. Only one of these characters is still a practicing Catholic, but all of them, and indeed most of the characters in the series, carry some kind of baggage connected to the Church. Lisa McGee's Northern Ireland is, as Catholic Irish-American Flannery O'Connor famously said of the American South, "Christ-haunted." However, each character's baggage is unique in ways that resist stereotyping. Dara remains a devout Catholic, while Robyn is an atheist, but it is Robyn who has a house full of children while Dara is a lesbian. In spite of their frequent bickering, they have the strongest friendship of any of the women; Robyn even accompanied Dara to Pride.
McGee's portrayal of Catholicism emphasizes the lower-case definition of the word: it is all-encompassing. Like Claire in Derry Girls, Dara is a Catholic lesbian whose storyline does not revolve around untenability of those two identities; her family accepts her and her church welcomes her without insisting she pass as straight. At the same time, neither show frames Catholicism in glowing terms. Their religious-themed humor is usually irreverent, and both shows feature nuns who are clearly agnostic. The single priest who appears regularly in either show is a vain fop. This ambivalence about faith is perhaps best characterized by hitwoman Booker in How to Get to Heaven: "I don't do business in God's house; I don't trust Him."
McGee's mastery of nuance is evident in the way she creates light-hearted comedies that center on deep historical wounds: The Troubles in Derry Girls and child abuse in How to Get to Heaven from Belfast. The Knives Out films seem to have lost their nuance along the way. All three have a nearly impossibly good protagonist who teams up with Benoit, but the family members in Knives Out are both villains and victims to varying degrees. The Glass Onion and Wake Up Dead Man pair their singularly good heroes with singularly bad villains and the sheep who mindlessly follow him and who never would have freed themselves without the brilliance of Benoit's insight. The third is the most black and white of the three.