Problem is, the games are the primary medium for Halo. Everything else comes after. Bungie made the story, characters, lore. They were never going to follow some novel written, because MS wanted to cash in on the CE sales/Halo hype, in 2001.
That's the only good thing going forward I guess is that 343 will oversee all Halo ventures. So that they can maintain cohesion between toys, games, movies, novels, comics etc.
Wait till you see how many Star Wars fans are going to shit themselves after Disney/Abrams forgo a lot of post Return of the Jedi expanded universe stuff in order to tell the story they want to. Obviously they wouldn't want to piss off many fans, so they might keep things fans really love, but it's going to really mess up the canon going forward and establish something new.