Is the senate present in the campaign?
If so, you will have always the missions, as they are hard-coded (afaik).
Thus, you will be able to reskin the factions, but for the game they will still be romans.
If I were you, I would start by trying to "separate" those roman factions from the senate. At first sight I only can think in a starting state of war between those factions and the senate (and consequently also the julii).
If you have eliminated the senate from the campaign, the task will be much easier.
Good luck!
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