John was declared dead following the events on Meridian. The decision was taken by ONI, and it makes sense. They couldn't simply admit that humanity's hero, a guy who almost single-handedly ended the Covenant threat, went rogue. Not only would that be very demoralizing, but it would also lead to mass panic. Better to claim he's dead.
"All Hail" and "The Cost" were supposed to be metaphorical, not literal interpretations of what was to happen. I agree that it was overkill given that the Chief and Locke do not stay enemies for long in the game, but I understand where the intention came from.
The shooting at the diplomatic meeting happened before the events of Halo 5. The whole Hunt the Truth campaign was a way to talk about events surrounding the plot of Halo 5. They couldn't talk about the plot, so they developped lore around it. On one hand, it can be misleading, on the other, it's a great way to create more lore without spoiling the game.
Remember that live-action trailers and marketing operations such as Hunt The Truth are usually in great part made by different people than those who write the game. Sometimes it's all 343's marketing team, sometimes there's other companies contracted for those jobs too. It does not justify the lack of coherence, but it explains it. The writers at 343 simply needs to take more time to check on what the marketing teams are doing.
I understand - and, to some extent, agree - that the marketing was somewhat misleading. Yes, 343 overplayed the John going rogue thing in their marketing campaign. Still, Hunt the Truth season was a smart way to introduce the global context of the game without spoiling it. Not everything about Halo 5's marketing was bad or totally unrelated to the game in my opinion.