Life's a game. How do you play?
I agree with the people that say "civil war". It would be just like here on Earth, with the schism between Shi'ites and Sunnis over the caliphate. On the one hand, you have the Prophets, who for all this time have named themselves the sole interpreters of the Forerunners' will. Then you have the humans, who the actual Reclaimers, as it would happen. This would have led to the Great Schism on a much greater scale. This also begs the question: what happened after Halo 3, when the Covenant was all but destroyed, and an uneasy peace settled throughout the galaxy?