The Assassin's Creed series has strong connects with some biblical things. I am not sure how far they will go with it, but a few of the mysteries seems to focus on Adam and Eve, whom Desmond is rumored to be descended from. You can see this in 'The Truth' which is a video unlocked in Assassin's Creed II showing Adam and Eve in what some believe is the Garden of Eden, free running with a Piece of Eden.
[video=youtube;CfA1Da8R2pU]http://www.youtube.com/watch?v=CfA1Da8R2pU[/video]
With this, I don't think your idea is that far fetched, I don't know much about bible stories. It might not work as a full game, but maybe a hidden memory or something could include a biblical memory. Whatever it would be, it would somehow have to be connected to Desmond's story or wherever they want to take the franchise after his story is over. If Adam and Eve were the first Assassins, a few other stories could come out of that. I suppose it could work, but Ubisoft might not want to focus a full story on just that.