Something else I've wondered about that, where/when did the Prophets lies about the great journey begin, when Truth, Mercy and Regret reactivated the Keyship's Monitor or at the begining of the covenant closer to the time of Legends: The Duel?
Also, were it just the Hierarchs and a close few others or was it every San shy'um aware they werent being completly forth-coming.
Since everyone else's answers are jumbled, I'll put it in better terms.
It started back during the origin of the Prophets. They were split about how they should go about using Forerunner artifacts, namely a keyship. Eventually, one side decided to barricade themselves in the keyship and leave, tearing a huge piece of rock out of their planet and creating the "foundation" of what would become High Charity. Later, the Prophets encountered the Elites, culminating in the Sangheili-San 'Shyuum War, where the Elites revered Forerunner artifacts and did not touch them, while the Prophets used them for their own benefit. This lead to the Prophets having an overwhelming technological advantage, although they could not gain a foothold outside of space battles. Eventually, with the Prophets realizing that they would need the Elites as protectors if there were other species as tenacious as Elites in the galaxy, and the Elites fearing extinction (likely through or initial bombardment) they eventually signed peace accords. This cumulated in the Writ of Union, the foundation of the Covenant. In the process, the Prophets convinced the Sangheili leadership that they were using Forerunner technology to propel them into a "Great Journey", like someone said, was another misinterpretation of an artifact they likely previously discovered. The Prophets would study and put Forerunner technology into a practical form, while the Elites would serve as their holy protectors and use the technology derived from Forerunner ruins. This, technically, at first wasn't a lie. Both were thoroughly convinced of it. Later, however, Mendicant Bias (the AI aboard the Keyship) got fed up with their shit and told them they had misentepreted a glyph, which they thought had said "reclaimation", after Humanity was found at Harvest. Humans showed up on their Luminaries (they basically were computers that scanned for Forerunner artifacts) as Forerunner artifacts. It had in fact said "reclaimer." The three prophets (Truth, Regret, and Mercy, while not known as such at the time) knew this would fuck the Covenant as splinter it, so they kept it a secret, and decided to commit genocide against Humanity to keep the Covenant from imploding. Eventually the Great Schism came and that all went to fuck, and we know how that turned out.
To answer you question, it was just Truth, Mercy, and Regret that knew the truth about Humanity. Nobody else was told or even learned of it until the events on Threshold, and later Installation 05.