it's really not about the lord at all, i think you're taking the title too literally:
http://www.seeklyrics.com/lyrics/Leonard-Cohen/Hallelujah.html
There are three versions of "Hallelujah" done by Leonard Cohen. The one you linked to which is on the album "Various Positions"; another version that is done live on "Cohen Live" ten years after the original version, and a third version which is a mix of the two, that he is currently doing on tour.
Supposedly Cohen wrote some 80 verses over a 5-year period for this song.
John Cale has said that Cohen gave 15 verses of the song to him.
From what I understand, all the cover versions that are out there are a mix of both versions: some lyrics from one and the the other.
Some say that the original version is "Biblical" and the live version is "secular", if the song is supposed to be a religious one, with lyrics like this:
"...Yeah but I remember, yeah when I moved in you,
And the holy dove, she was moving too,
Yes every single breath that we drew was Hallelujah..."
I may have to consider changing churches.