I'm not aware of Amy Ray ever explaining the meaning of this song, but what I get from it is commentary on being gay and interacting with Christian churches. The phrase "strange fire" comes from a puzzling biblical passage theologians have often struggled to make sense of in a modern context. It describes two sons of Aaron who bring an offering to the altar, and their god not only rejects their offering, but kills them for it:
Leviticus 10:1 reads: And Nadab and Abihu, the sons of Aaron, took either of them his censer, and put fire therein, and put incense thereon, and offered strange fire before the Lord, which he commanded them not. And there went out fire from the Lord, and devoured them, and they died before the Lord. So what is this "strange fire"? Modern interpretations say that Nadab and Abihu brought incense that had been lit elsewhere, disobeying a rule that only incense lit at the altar itself could be offered.
Amy connects herself to the incense with "the incense of my soul is burned/by the fire in my blood." What's her offering? Her love. "I make an offering of love/I come to you with strange fire."
Yet, the church rejects it. It tells her she's brought the wrong kind of love. I'm interpreting here, but I think that she's probably referencing her sexuality - she offers up what's in her soul, and she's told it's wrong. She puts herself in the shoes of Nadab and Abihu here.
She goes on to condemn the preachers who've rejected her, with her "mercenaries of the shrine/now who are you to speak from god?" She ends in a place where self-love helps her get over the rejection "when you learn to love yourself/you will disolve all the stones that are cast." There she finds "a peace that will take you higher." And it doesn't come from rejecting her own sexuality, but embracing it. At the end of the song, she's still saying "I come to you with my offering/I bring you strange fire." So she's not adapting to the church's view that her offering, her love, is wrong. She's defiantly embracing it and challenging others to explain how they can possibly speak for god in rejecting it. It's a gorgeous, painful song, and my interpretation of it isn't based on anything I've ever heard Amy say. From: https://songmeanings.com/songs/view/3530822107858880503/
