To me this sounds like just a tragic case of someone (the narirator) loving someone almost too much who does not feel the same way about them. And though they wish and 'pray' if you will, those feelings don't change.
And for the second half of the song it almost sounds like they are trying to distract themselves with lies, ex: "There is another love that I would rather be obeying"
And overall it sounds like a song of desperation, denial and rejection.
It's a beautiful song and I can't get enough of it.