I understand your concerns - and I know that it's an enormously ambitious project, just from a writing perspective.
The Shivans will have some truly terrifying reasons for their genocidal onslaughts. They're not going to be doing it just out of survival, or out of fear, or because of some scarring event in their species' past. They won't be after some singular objective that, after accomplishing, they'd leave us alone. Most importantly, they're not going to be mindless killers, and they're definitely not going to be insane psychopaths. They're going to be able to justify their actions as right - to the point where the GTVA will not be able to claim the moral high ground. And yes, they will be just as relentless as they were in Freespace 1 and 2.
Ultimately, it's going to go back to that line from Freespace 1: "The great destroyers are also the great preservers," but this time, taken further. The Shivans perpetually destroy, in order to create. They are not the preservers of the present, but instead, preservers of the future. They destroy because it's the right thing to do.
Also, from a strategic perspective, I'm going to reveal the actual sources of Shivan warships. They don't have planetary shipyards and such, like the GTVA. They have to build everything out in the vacuum of space. Shivan supercarriers can manufacture fighters and bombers by the hundreds, and the Shivans' mobile colonies act as supersized versions of the GTL Anemoi / GVL Tawaret, but with the capability to build new warships.