Superfaction also creates the roman-style-unbreakable alliance, apart from the missions and also affects the way the AI handles a faction. Afaik factions that are part of a superfaction system need to belong to the same culture. Still, as MonkWarrior has said iirc (researched in their Iberia:TW) the whole system is somewhat unstable if not used for romans.

If you simply remove the superfaction lines from the 3 roman factions, then you won't break anything.