i don't think they'll do sub factions for this story line, in fact it would be fairly hard to do sub fractions at all. introducing new factions such as flood and sentinels they could do but only in another game (Halo Wars 2 if or when they make that). the only factions i think they could possibly have in the games are UNSC, Covenant, the Rebel lot of both Human and Covenant, Flood and Sentinels (maybe Elites as a separate bunch if they make a Halo Wars game set after Halo 3) and none of them are really what i would call "sub factions" of any of the others.
ORDINATOR the Lekgolo Jager