Not hard to figure it out, Peter.
I'm sure he meant it to be about David & Bathsheba, and about sex, and about relationships. Once a song gets out in the world, though, it had different meaning for different people. I personally find the belief that just because the word "hallelujah" is in it, it must be a religious song, a bit amusing, and a bit annoying. Suuuure, the Jewish Zen Buddhist monk wrote a Christian hymn. But, like I said, it's open to interpretation