Bungie actually said "We hinted at it off and on and then even had Spark outright say it." So yes, it is actually what they intended.
-- Citation needed. (Seriously, I would like to see where this was said, for reference.)
-- That was clearly one of the directions of the story, at one time. I don't know you could possibly interpret what Bias says in Contact Harvest any other way. But I think you are overestimating how much Halo canon was set in stone from game-to-game. Especially when it comes to the novels, which were usually apocrypha as far as Bungie was concerned.
But then 343 goes and screws it up and says that the fake pretense that I talked about was actually the real reason and the humans were just some other group.
-- Humans and Forerunners are still very closely related post-Forerunner Saga, having been branched off from each other by the Precursors at some very early date.
Gah, it makes me so mad!!!!!! You had this awesome, beautiful, intricate story, and then you just mess it all completely up. The prophets actually had motivation then. Motive. 343's uber, sickeningly cliche move of making them another alien race radically cheapened the motive that Bungie specifically designed the prophets to have.
-- I'm a bit shocked that you don't think the tired old trope of
Humans themselves being the Precursor race was worse than the Forerunners being closely related cousins.
Maybe they can fix it by saying that the didact and librarian and all those were actually deformed/evolved/alien-hybrid individuals? Maybe?
-- The crystal ball is showing "Unlikely."
The good thing about 343 going forward is, that by overseeing all development now, they can integrate their toys, books, and games as one and promote a unified story. No more crying because Bungie didn't follow some book written decade before that they never really gave permission for/wanted because Microsoft made the decision etc.
-- Aye, but this isn't an easy thing to do given the different tones, authors, and time periods that this material falls in. Bungie themselves played really fast and loose with canon in ways that are not always immediately obvious if you just play the games and consume nothing else (e.g. the totally different layout of New Mombasa between Halo 2 and Halo 3: ODST).
-- Halo 4 jackals are a phenotype hailing from a different region of their homeworld (Ibie'sh, see
Halo 4:The Essential Visual Guide, p. 40).