Yeah, I think that part works already. As has been pointed out, there are a number of missions in both FS and FS2 where Shivans attack HOL, Shivans attack NTF... In the first mission in FS1 where Shivans are encountered (where you escort the Plato), hostile Vasudans jump in, then the hostile Shivans pop in and kick the crap out of them, then come after the Plato.
I think FRED will ***** about it (saying you're attacking ships on same team), but the AI code seems to do it correctly... I am assuming that in the missions in question, the Shivans have goal SEXPs directing them to attack the other bad guys.