Removing that line from all IDs sounds ideal, especially in scenarios where most factions would likely temporarily ally with one another in order to defeat a common foe. Perhaps certain IDs could have the line altered instead of removed, for example in the case of the Corsair/Hessian ID. "Cannot ally with Hessians/Corsairs under any circumstance" may be a good idea, since they've been at war for centuries.
Similarly, maybe any ID that references "May hunt X faction anywhere" should also have a similar limitation? I'm just pitching ideas out here.