
I haven't noticed any departures in the comics from the Halo story as told in the games. They seem to be very careful about not changing anything.
I did have an issue in the Karen Traviss novels when they arrested Halsey and treated her like a criminal. I didn't get the sense that she was so evil or solely to blame for the Spartan II program from the earlier novels, or even in Halo Reach where she makes a brief appearance. I think 343 Industries and Mrs. Traviss did a bit of revisionist history in order to take some moral high ground on how it's bad to abduct children for your army (maybe to clean up the story for mainstream appeal). I think something like that had to have been supported by more than one person in the UNSC. Halsey being a villan just rubbed me the wrong way. I mean, she's not like that in Eric Nylund's Fall of Reach book. She's actually quite likable and has a conscience about what she and the UNSC are doing to create Spartan warriors.