Let's calm down, people. Nobody wants to get banned.
First off, the Sathanaseses could not have escaped the supernova and remained in-system. There's simply no way. The mission is titled Apocalypse. The final mission of the game. The supernova is portrayed as a massive wave of destruction, frying ships and planets, wiping the system clean of life. It's pretty clear that the developers intended the supernova to devastate everything, representing the complete obliteration of an entire star system. For the juggernauts to have remained in Capella, surviving on a technicality, is quite unlikely.
Second, there is absolutely no reason to doubt Petrarch's hunch. It's the end of the game, and it's the only canon explanation provided for the inexplicable act of ignoring enemy forces and blowing up a star. As karajorma said, why would they lie to us then, after we completed the game? Petrarch as a character may be fallible, but as the one delivering the epilogue, there's simply no way.
However, perhaps Capella was an accident. That's certainly possible. Remember that juggernauts, the very same ships that engineered the subspace wave, were also destroyed in the blast. If the juggernauts were built with the express purpose of creating massive jump nodes, why would the Shivans allow some to be destroyed every time one was made? Surely they would have anticipated that? They have the technology to create nodes from stars, but each time part of the fleet gets obliterated? I think not. The motive, clearly, was not to hurt the GTVA, because the eighty juggernauts would have wiped the floor with the entire fleet without breaking a sweat. Thus, it cannot have been a sacrificial ploy to destroy the allied fleet. They were winning. What would possibly motivate them to blow up half their fleet in a supernova? Nothing, that's what!
Now. To say that the Shivans, masters of subspace and of bizarre technology, completely screwed up their uber-jump node on their own, allowing their jump-node constructor armada to be partially obliterated, is ridiculous. The Shivans know more about what they did than we do, how could they allow such a catastrophe to occur? Absurd! It's impossible for the Shivans to have messed up so badly, right?
There is one way.
Before the juggernaut fleet came bearing down on the GTVA, there was one event that could have put their plans into disarray. One component that was missing. One, and only one reason for the supernode to fail so spectacularly, causing the Capella incident. Yes, the one Sathanas-class Shivan juggernaut that was missing from the fleet, the single node constructor that was destroyed by the GTVA! One single juggernaut arrived early, and fell victim to the guns of the Colossus! That was all it took for only partial success to be possible, for part of the fleet to escape and leave the rest to their fiery grave!
The Shivans must have known about the destruction of the first Sathanas. They lost contact with a huge, powerful ship, one of the most important in their fleet, the first one to arrive, the only one not present. How could they not miss it? If its absence was indeed the cause of the supernova, wouldn't the Shivans have known how important it was to have all ships present? It's their technology, after all. The Shivans must have been desperate! For some reason, returning home, and returning home now, was important enough to risk massive casualties! What could possibly have motivated the Shivans to attempt a supernode with insufficient ships? Could there be something...else...? All we ever got from Volition, the one explanation for the Shivans' bizarre actions, was that the Shivans were a symptom of a much greater problem...