One of the things that attracted me to the first Halo series was the humanity of the writing. Halo (especially the first one) never glorified violence in the lore of the game. There is much lamenting the horrifying situation that Master Chief finds himself.
This is of course completely lost in multiplayer, but I'm not sure how you can blame bungie for the non-authored parts of the game.
Well, Bungie has some good writers, but the very concept of the game they created is inherently xenophobic. You're pitted against an Other who exists only for you to kill. Eventually, you are allowed to see that this Other is more complex than that, and therefore maybe not worth killing unnecessarily, but now you have a new Other to mindlessly kill, and there's not a whole lot of awareness that there's an irony to the change.
The story of a game is told through gameplay, not through cut scenes in between. The gameplay of Halo is, "kill these things". Not much more complicated than that. The writing can self-pity itself as much as it would like, but the fact remains that Bungie created a game in which there is only one possible course of action, and that is to kill. That multiplayer is such an aggressive shitpile, legendarily so in Halo's case, only goes to show that beneath the facade of "story" in Halo, there is pretty much just "shoot things and feel like a badass for doing so, or else get pissed off that somebody is better at shooting you than you are for them."
Jonathan Blow, who's a brilliant game developer in his own right, gave a lecture in 2008 about exactly this sort of dissonance between storytelling and gameplay. He does a great job pointing out that even the best titles in gaming, like Grand Theft Auto and Half-Life, do a poor job of aligning in-game story with the actual play. It's long, but if this is a subject that interests you, then it's absolutely worth giving a look: http://www.youtube.com/watch?v=mGTV8qLbBWE. (Whilst studying this subject for my undergraduate thesis, I also took notes on this whole lecture, so if you're feeling lazy I could upload them for you; let me know if you'd like that!)
This is of course completely lost in multiplayer, but I'm not sure how you can blame bungie for the non-authored parts of the game.