The whole movie is infused with catholicism -as a perfect mirror of reality. The community lives a religiocentric-life. Even if we think about the church's physical location within Andean towns, it's always in the middle of the space, right beside a park. The calendar is distributed according to religious holidays. Andean life cannot liberate from church.
Noe's work depends on it. He's a worker of God. The whole family is close to the parish priest. Despite that, the community uses religion as an excuse for his punishment. Religion is entangled with sexism and homophobia. It has been adapted from its former state to fit the conqueror's means. It is a tool to colonize our bodies/minds. So it is evident but still shocking -especially visually- the reaction of society. Since hatred towards queerness is an imposed concept, their actions are violent. If they had a reason -outside of religion- to hate diverse genders and sexualities, brutality would not be the primary reaction. Indigenous communities rely upon orality, so a conversation presides an action. In an idyllic reality where the conquest would not have happened, Noe would not have had to kill himself. But that is not the case. The system wants to "Exterminate All the Brutes", "Kill the Indian to save the man", etc.
Still, Segundo breaks up with tradition and religion at the end of the film. At first, when he finds about his father's sexuality, he reproduces the colonizer's modes, but he is different. He is not afraid to feel. So he embraces his father, even when Noe cannot do the same for himself.