Yeah, I think the element of history cycling around is pretty strong in Freespace. I hold that the strongest explanation for the Shivan actions is fear - the GTVA is an unknown threat to them, that has managed to match the technology that had once been the Shivans' strongest asset. They have no idea how much stronger they are than us, so with Capella they simply choose the safest (to them) course of action - to block off the Capella system permanent so the Gamma Draconis node cannot be used.
Also, the Vasudans are heavily implied to be related to the Ancients, so the Shivans have special reasons to fear them. (This, I think, is why Bosch thinks that he can get the humans to ally with the Shivans by abandoning the Vasudans.) To the Shivans, the GTVA represents the return of their old nemesis, only now technologically stronger than ever. Of course they are scared ****less of us. Throughout the series, we see from the perspectives of the humans and the ancients, who see the Shivans as godlike beings of destruction. But with the Shivans, they've had thousands of years to dream old nightmares about the Ancients somehow surviving, somehow coming back, somehow figuring out their tricks and defenses, somehow punishing them for their own old crimes.
When Bosch went to communicate with them, just after the first Sanathas was destroyed, and the Shivans learned that the GTVA had at least one Juggernaut class ship, the Shivans probably thought the GTVA had sent an envoy to dictate terms for Shivan surrender.