"THIS IS NOT RECLAMATION, THIS IS RECLAIMER, AND THOSE IT REPRESENTS ARE MY MAKERS" - 032 Mendicant Bias
This quote singlehandedly guaranteed the mass genocide of Humankind, for the Covenant must be upheld, and the Prophet's position as holy interpreters must prosper. But by putting together the pieces of certain words spoken by the Hierarchs themselves, one will see that the need to dismiss Humanity as completely unrelated to the Forerunner was not entirely necessary, that the to-be Hierarchs could have fashioned a much more intricate lie. Another quote proves this assumption.
"Soon the Great Journey shall begin, but when it does, the weight of your heresy will stay your feet" - Prophet fo Truth
In saying this, Truth guarantees two things; Not all can partake in the glory of the Great Journey, and the same could be said for the Forerunners. So what if the Humans were Forerunner? They would have been rebels, heretics on the run from the "holy" Forerunners, they were then left behind during the activation of Halo. The Prophets could justify all this in the faith clouded eyes of the Covenant's leaders. Perhaps they thought it more suitable to maintain the Forerunner image as gods incapable of heresy against themselves, but I'm sure they would have been able to smooth it over with the deluded members of the High Council. In doing this, they could have excluded the Philologist from their group of three, adn picked a much more suitable candidate, do why not? The lies would have been part truth, and would not be questioned.