I have come to a set of three possibilities regarding the voice the Archbishop is hearing, because I highly doubt someone who wants to save the world would also hand out the recipe for the blood sacrifice device that it needs to be saved from.
His connection to the Goddess has grown stronger over the years, to the point where he's inadvertently hearing her frustrations. This would explain the "everything is flawed" in the Goddess's voice, since she'd probably have to vent at some time, but it doesn't explain the blood sacrifice slave collar manufacturing device.
His connection to the Goddess was either usurped by or always came from an Evil God. This one does introduce another entity of comparable supernatural power to the story, which is a tough sell. This would also require the evil to either be a new arrival, something subtle, or a story the Church has forgotten.
The Goddess has two sides, one good and one evil, and the evil side managed to get control of the conduit to the Archbishop. Admittedly, this is a pretty Jekyll-and-Hyde thing to have happen, but it would be easy for the evil half of the Goddess to sound like the good half.
We do, however, know that the Archbishop isn't acting as the Goddess actually wills because she sent Rikimaru and his human to do something to stop him.
