I'd bet on it, just because even with the new status quo, the member species of the Covenant are probably better off together than they are apart (especially the Grunts.) There was a reason they formed into their own "new Covenants" in the first place.

Also, the Covenant are still great from a gameplay perspective, and apart they aren't as interesting (although it'd be wild if we started fighting Jackals with a wider variety of combat roles, same with Grunts... in fact Halo 5's heavy use of the jetpack Jackals makes them far more tenacious than previous games. They'd constantly get behind me and pick me off in Blue Team.)