I agree with Admiral Wolf, only a few juggernauts were lost (as seen from the cutscene). The Destroyers, Corvettes, and other ships caught in the supernova were, as many have said, expendable.
Now then, in response to Marcus Vesper, you could have stuck a fork in the GTVA prior to Capella because they were done. They knew it, the Shivans knew it, and anyone watching the conflict would know it, too. Even if the GTVA would have fought to the bitter end, victory was assured the moment the Colossus went down. A single Sathanas destroyed most of a GTVA fleet (remarked if you fail to get all beam cannons in Bearbaiting) by itself so the chances of the GTVA somehow taking down even a few juggernauts with Destroyers and Bombers borders the impossible. Even if the Shivans knew that the Capella nodes were being collapsed, they could still plant their flag in Terran-Vasudan space and know they own that territory.
I read Snail's Theory and like it, though I add a caveat to the whole Hive-mind thing (which somewhat resembles Warhammer 40k's Tyranids). While I agree the Shivans are Hive-minded, they were created that way to serve as the ultimate fighting force. They will always win the war of attrition because they have no morale to break, they outnumber their foes 10:1 and they have technology that rivals or surpasses everything they encounter. They are relentless.
On the other hand, I believe they're on a leash. It wasn't until the Ancients began conquering the galaxy and raising hell via subspace that the Shivan hounds were released. With tech that rivaled the Shivans, the Ancients put up a fight but they never had a chance to win. The same goes for the Great War with Terrans and Vasudans fighting previously and sending great fleets through subspace. It is my belief that Lucifer fleet was a slap on the hand to tell the Terrans and Vasudans to play nice and in doing so, forged an alliance between the species that also ended the war.
The Sathanas fleet incursion was merely a show of arms. The GTVA thought they were high and mighty with their flashy juggernaut and beam cannons and with all the subspace activity to crush the NTF, the Shivans were brought out again to put the Terrans and Vasudans in their place. They were not originally out to conquer Terran-Vasudan space but when the GTVA began assaulting them, they acted in self-defense. The destruction of Capella had two purposes: 1.) to crush the morale of the GTVA via a display of power and 2.) tell their masters that the mission was accomplished.
The Masters, as I have coined, are actually benevolent and the Shivans are simply their army. When Bosch communicated with the Shivans, he learned that the Shivans were not out to destroy but to subdue. The Ancients were out of control and had to be put down by the Shivans but the Terrans and Vasudans were given a chance to correct their mistakes and keep surviving. Without some kind of unseen power keeping the Shivans at bay, there is no way the GTVA would have survived as long as it did.