In my opinion, that's a great song. Beautiful melody, great expression in the singing and good poetry.
The bridge in the middle is a particularly haunting melody.
Effective writing often uses metaphor, and the phrase "take me to church" has morphed into an idiom that need not be taken literally to convey a message.
Trying to have a religious conversation within the context of this song is misguided.
By the way Jasmine Thompson does a great cover of this song if you want to hear how a woman (actually a very young woman) interprets the song.