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VATICAN CITY, VATICAN - MARCH 29:  Pope Francis waves to the faithful as he leaves St. Peter's Square at the the end of Palm Sunday Mass on March 29, 2015 in Vatican City, Vatican. On Palm Sunday Christians celebrate Jesus' arrival into Jerusalem, where he was put to death. It marks the official beginning of Holy Week during which Christians observe the death of Christ before celebrations begin on Easter.  (Photo by Franco Origlia/Getty Images)
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VATICAN CITY, VATICAN - MARCH 29: Pope Francis waves to the faithful as he leaves St. Peter's Square at the the end of Palm Sunday Mass on March 29, 2015 in Vatican City, Vatican. On Palm Sunday Christians celebrate Jesus' arrival into Jerusalem, where he was put to death. It marks the official beginning of Holy Week during which Christians observe the death of Christ before celebrations begin on Easter. (Photo by Franco Origlia/Getty Images)
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Editor’s Note: Jill Filipovic is a journalist based in New York and Nairobi, Kenya, and the author of the book “The H-Spot: The Feminist Pursuit of Happiness.” Follow her on Twitter. The opinions expressed in this commentary are solely those of the author. View more opinion articles on CNN.

(CNN) —  

As long-simmering tensions in the Catholic Church again boil to the surface over allegations of child sex crimes, a prominent – and controversial – archbishop is calling for the Pope’s resignation. Is the church confronting a coup, or is it finally facing a reckoning?

It’s both.

Jill Filipovic
PHOTO: Courtesy of Jill Filipovic
Jill Filipovic

Of course, the church needs to be held accountable for the scandal – up to its highest leader. But there is little evidence that the new calls to oust Pope Francis are being made in good faith over genuine concern for children abused over decades – or the culture of male impunity that enabled it.

No, this current wave of outrage is led by the conservative clergy, via a recent 11-page later from Archbishop Carlo Maria Viganò – the former top Vatican diplomat in the United States, who Francis chose to replace. Viganò alleges that a “homosexual current” led to the sexual abuse scandal and that Francis covered for a cardinal he knew was a “sexual predator.” The Pope’s response: “I will not say a single word on this.”

It is important to note here that Viganò and other doctrinally conservative Catholics don’t like the Pope’s more progressive doctrine: things like caring for the poor, speaking out for immigrants, and easing up on the animosity toward gays and divorced women. In fact, those same conservatives have defended and even promoted the very aspects of the Catholic Church that allowed sex abuse and other appalling treatment of children to thrive: lionizing male power, subordinating women, and stigmatizing homosexuality.

Now they’re using new sex abuse allegations as ammunition against a pope they believe is too permissive.

It’s a drama in which there is no one to root for.

Pennsylvania Attorney General Josh Shapiro told NBC’s “Today” show Tuesday that the Vatican knew about the sex abuse allegations in churches across his state, though he did not say when the Vatican learned of the allegations. Whether Pope Francis was personally aware is less clear, but as the leader and figurehead of the church, the responsibility ultimately lies with him – as it did with his predecessor and the man before him, both of whom faced no consequences.

It is long past due that the head of this institution answers not just for the priests who spent decades abusing thousands of children, but for the institution itself spending millions to fight accusers and cover its own tracks.

But removing this Pope in exchange for someone who will please more traditional Catholics is hardly the answer. This abuse, and the system that covered it up and perpetuated it, did not exist in a vacuum. It is a direct outcome of the church’s patriarchal structure and its fundamental bigotry.

After all, despite this Pope’s designation as a “liberal,” he still oversees an institution that discriminates against women so blatantly and unapologetically that, were it not a religious organization, it would run afoul of American anti-discrimination laws.

No institution, and no person, deserves the designation “progressive” if they treat women like second-class citizens, refusing to allow us to occupy the same positions as men, and putting us in a kind of separate and unequal category of human being.

I was raised more twice-a-year-Christian than Catholic, but much of my extended family is (or was at one point) Catholic. Had I been raised in the church, as my mother was, this built-in misogyny would have been enough to push me to leave long ago. I cannot reconcile feminist and progressive values with an institution that treats women with this kind of contempt masquerading as devotion.

Indeed, this impacted my own family: When my grandmother, a survivor of domestic abuse, finally left her marriage and found herself a single mother of five young children in the 1950s, the church turned its back on her. My grandfather, on the other hand, remained enough in its good graces that, years later, he was able to get his marriage conveniently annulled so he could remarry with the church’s blessing.

The church’s misogyny has led to some of its worst abuses. Sex abuse of altar boys rightly made headlines, but girls were sexually assaulted and raped, too. And boys were abused in large part because of the fact that ingrained Church sexism gave priests easier access to boys than girls – until relatively recently, girls couldn’t be altar servers. The all-male church power structure meant that priests got more alone time with young boys, and the church’s own misogyny and homophobia compounded the shame and silence that so many abused boys carried into adulthood.

Catholic patriarchy didn’t just beget priests who sexually assaulted children. Around the world, the church branded unmarried women immoral, treating them like social contaminants and hiding them away in shame. Some of the children of unmarried women wound up in orphanages, and suffered greatly – beaten, starved, mutilated. Some of them died, allegedly at the hands of neglectful or abusive nuns.

And still today, the church opposes the rights of women to decide when and whether to have children – even contraception is forbidden. Women’s bodies aren’t theirs; they are vessels for male prerogatives. Is it any surprise that an institution in which this view of women is deeply ingrained is also an institution in which sexual assault – a crime in which one person believes they have total authority over another’s body – flourishes with little consequence?

No institution can totally immunize itself from abuse, but it can either foster or discourage the conditions for it. The church fostered them. And so, yes, the Pope should pay a price – probably with his job. But so should every other male authority figure in the church who has worked to uphold unfettered patriarchal power and to keep women in positions of subservience.

Which means, of course, that the entire church must radically reform – and if it doesn’t, decent Catholics must decide that keeping with their faith demands abandoning this noxious institution.