Here's a fuller explanation than in the last post - from The Watchmen Director Zack Snyder:
Crave Online asks: "What about the Leonard Cohen song?"
Zack Snyder: "There are two Leonard Cohen’s because there is a Leonard Cohen on the end titles as well. Hallelujah, that love scene, I originally had the Allison Crowe version of that song, a version I’ve always loved, but in the end was just too romantic. Everybody thought that I meant it. They thought the love scene was serious, not that it isn’t serious but her version was too sexy. So I was like yeah, I’ve got to go back to the Leonard Cohen. For me it is incredibly ironic, even with that version of the song it is incredibly ironic. I don’t care what version of Hallelujah is on, that love scene it is ridiculous, but in a great way. With Leonard Cohen it is like you can’t miss it now, can you? I’m sure some people will but that is fine."
http://www.craveonline.com/articles/filmtv/04653139/2/zack_snyder_talks_watchmen.html