Totally agree with the WB view on this.
A game based on the Year One story just wouldnt work. In the word of Bruce Wayne himself from Year One, when he makes a mess of his first night in the Cowl, "F'ing Amateur", his first year is made up of mistakes as he finds his place as Batman and that as a game would feel weak, a Batman that can make mistakes?
Origins is doing the right thing, its a blend of themes from Year One and Knightfall which gives the Arkham version of Batman more for the player to do and experience then if you allowed the player to relive his very first year. This way in Origins, as the player you can see Batman not yet at his prime but not so Amateur that you would expect him to fail as he finds his feet. A Batman 2 years into his "work" meeting new villains for the first time is a great setting for both the game and the story that WB wanted to tell.
As a fan of Bats from the comic books to animation, movies and now the Arkham series, it all makes sense