I think that after the leading Prophets were revealed to be misleading the masses, by one of the warrior caste no less, their religious(?) sway would be rejected outright and all of the covenant species would be more open to including humanity. Sure there would still be hard feelings within the Covenant factions about the things that happened during the war on both sides, But there would be more to gain from each other than from destroying each other.
It seems to me that the common denominator that all of these different races had was The Great Journey. After this was revealed to be in essence, a whole lot of horse-s##it, humans would probably be brought into the fold. But then there is the whole enemy of my enmy thing... in which case the elites may choose to continue the war our of some racial motivation.