Like I said before, it's very strongly hinted that the enemy in the game aren't the helghast themselves in entirety, but rather a terrorism group within them intent on bringing boiling tensions to the breaking point and sparking out and out war.
There's a lot of potential in this premise, as we could (hopefully) see each sides respective leader playing a delicate game with one another to placate their populace while also averting war and working with one another.
Similar to the relationship on the President and the Kremlin during the Cold War era.
Shadow Marshals probably aren't there to keep the peace directly. They're a designation that has existed since Killzone 1 for their special black ops infiltration troops. The Helghast would have an equivalent, but they wouldn't be a shadow marshal. Shadow Marshals are meant for far more than peace, but that probably will be your overall goal in the campaign. It wouild be even better if, and this is predicated on there being two campaigns, both the Helghast and ISA character have to work together.