From a March interview with the artist published in New York Magazine:
“Take Me to Church” is a critique of oppressive institutions, with a woman or female pronoun used as a sort of savior.
“Take Me to Church” is essentially about sex, but it’s a tongue-in-cheek attack at organizations that would … well, it’s about sex and it’s about humanity, and obviously sex and humanity are incredibly tied. Sexuality, and sexual orientation — regardless of orientation — is just natural. An act of sex is one of the most human things. But an organization like the church, say, through its doctrine, would undermine humanity by successfully teaching shame about sexual orientation — that it is sinful, or that it offends God. The song is about asserting yourself and reclaiming your humanity through an act of love. Turning your back on the theoretical thing, something that’s not tangible, and choosing to worship or love something that is tangible and real — something that can be experienced.
But it’s not an attack on faith. Coming from Ireland, obviously, there’s a bit of a cultural hangover from the influence of the church. You’ve got a lot of people walking around with a heavy weight in their hearts and a disappointment, and that shit carries from generation to generation. So the song is just about that — it’s an assertion of self, reclaiming humanity back for something that is the most natural and worthwhile. Electing, in this case a female, to choose a love who is worth loving.