Free Space/WMG

The Shivans blew up the Capella star because they feared the GTVA.
Looking at it from the perspective of the Shivans - out of nowhere, there comes a pair of unintelligible alien races. The most advanced ship sent to destroy them is itself destroyed, even though the Terrans and Vasudans had previously exhibited no weapons capable of even scratching Shivan technology. A followup mission afterwards showed the two races suddenly exponentially stronger than before, adopting technology on a par with their own (despite a several thousand year head start) and capable of making incursions into Shivan space. Worse, the newcomers seem to have access to Ancient technology, including the Knossos gate. (The Vasudans in particular are implied in various places to have close connections in the past with the Ancients.) And when they again send the most powerful class of ship they have at their disposal, the Sanathas, it gets destroyed by a Juggernaut class ship!

Imagine: the Shivans have been around as the top dogs of the galaxy for thousands of years, over which they probably made no real meaningful advances. When that kind of arrogant superiority complex breaks down, it breaks all the way down. To the Shivans, they have no idea of the extent of the GTVA - for all they know, the Colossus could be part of a huge fleet of Collossus class ships, set to invade. Plus the terrans can be assumed to have the jump node stabilisation technology. So, ironically, even as the GTVA sends the meson bombs to seal off the Gamma Draconis gate, the Shivans plan to do the same - sacrificing multiple Sanathas vessels to make the entire Capella system impassable, to prevent what they think would be a full scale invasion of the Nebula and beyond.

Of course, at this point, communicating with Bosch could have made them realise how close they actually were to victory, but by now the SOC had destroyed the shivan communications nodes so there was no way of calling off the Sanathas. The ending of FS 2, then, was a colossal and unintentional bluff, paying off on a huge scale. In the Shivans' eyes, the GTVA were now the Destroyers, the mysterious new race that just refused to die.


 * The one major issue I can find is that you are assuming that the Sathanas etc. al actually were the top of the line the Shivans had, which is questionable in and of itself (the sheer number they possessed would indicate that they have the resources to build something even bigger and more dangerous). That being said, even with that taken into consideration, the psychological damage could be inflicted anyway.


 * Actually, this also works in the reverse (as does any argument against this idea): how would Shivans have known that the Collosus was the biggest ship in GTVA's armada (the sheer speed of GTVA's technological developement "would indicate that they have resources to build something even bigger and more dangerous")? Also: how would they have known there was only one Collosus?

The Shivans aren't "the Destroyers"
Tangentially related to the previous WMG. The Shivans aren't actually the ones who destroyed the Ancients, but a different race.

The Destroyers are a nomadic race which destroyed (natch) the Ancients, then, encountering no more resistance, moved on to a different region of space. This region was inhabited by the Shivans, who tried to fight the Destroyers off but failed, since they simply kept coming.

So they escaped, fleeing through the stars, and eventually stumbling upon the region of space where the Terrans and the Vasudans had since evolved. After many generations of battles against the Destroyers without encountering any other races, it had become ingrained in the Shivans' minds that "aliens = Destroyers = bad", and therefore they saw the Terrans and the Vasudans as a new kind of Destroyers and attacked them without pausing to ask questions. This, basically, means that the whole war in the two games was caused by a failure to communicate.


 * Problem with this is that the scientist studying the Ancients found proof of Shivan weaponry.
 * Possible explaination: the weapons were actually the Destroyers' weapons, who used them against the Ancient. Then the Destroyers moved on, and used them against the Shivans, who had inferior weaponry but somehow managed to repel the first wave of attacks, and then scoured the battle wreckage and reverse-engineered the Destroyers' weapons for their own use. This could explain why proof of Shivan weaponry was found by studing the Ancients -- from a technological standpoint, the Destroyers' and the Shivans' weapons are almost indistinguishable.
 * Which makes this Guess even more awesome, as it fits completely with the "9 Cities of Troy" theme that is a series motif.
 * The guess also gels well with that old comment from one of the devs that the Shivans are "part of a much larger problem." Maybe the Shivans didn't originally evolve in subspace, but took refuge from the Destroyers in subspace and stayed for so long they developed more adaptations to it.

The Shivans are constructs created by the actual race of "Destroyers," who are just protecting their turf.
The Shivans don't behave like a normal species. They don't try to control planets or capture natural resources, instead being focused mostly on controlling jump nodes. They don't even attempt to communicate with other species. They can apparently survive in a vacuum, and it seems really implausible that they could have naturally evolved a beam cannon.

Note also their choice of targets: They specifically go after and try to destroy races that have both subspace technology and warlike tendencies. (The Ancients went around conquering everything before they ran into the Shivans, and the Terrans and Vasudans had been at war for decades.) It could be that some other race created the Shivans to send after any other species that could possibly become a threat to them.

The actual Destroyers have a huge empire that's really far away from GTVA space, and which normally does not have any connection to GTVA space via jump nodes. The Knossos portal device allowed the Ancients to access a system that was really close to Destroyer-controlled space, and they sent the Shivans to blow up the star; hence why it's now a nebula. This was the "one system" the Ancients described being able to forego. They shut down the portal to protect themselves, but the Lucifer fleet managed to get through before the jump node fully closed down. The fleet that attacked the Terrans and Vasudans in Free Space 1 was the same one that killed the Ancients; it's just been biding its time this whole time in systems that are a few jumps away via unstable jump nodes that the Shivans can still use, but they had been unable to return to Destroyer space. It's possible that by the time Free Space 2 rolls around, the Destroyers are still unaware of the Terrans' and Vasudans' existence or the destruction of the Lucifer fleet, since without a subspace link communications would have to rely on light speed.

When the NTF reactivated the portal, the Destroyers took notice and sent whatever ships they had in the system at the time to investigate (the Ravana and the first Sathanas.) When those ships got destroyed (and they found out that the Lucifer fleet had been as well), the Destroyers freaked and went back to the "blow up everything" plan. Since it was just a bunch of constructs and the Destroyers' empire had virtually unlimited resources at its disposal, they were okay with losing a few dozen Sathanas ships per system if they had to. They ignored Gamma Draconis since there was nothing in it and went for Capella. Had the GTVA not sealed off the system, the Destroyers would have eventually destroyed every inhabited system. (Sol, being cut off from everywhere, would have been safe.)

That throwaway line in Silent Threat about the GTI knowing about the Shivans before Ross 128 is more correct than the character speaking it thought.
Specifically, GTI knew about the Shivans even before the Vasudan War started, and this is why it's so easy to reverse-engineer Shivan technology; the GTA is already flying watered-down Shivan technology, secretly discovered, reverse-engineered and quietly disseminated into standard use. This is why many frontline Vasudan fighters are so piss-ass weak compared to their Terran equivalents during the T-V War/Great War; compare the Anubis to the Apollo or the Seth to the original Herc. Of course, the Vasudans are far more graceful engineers, which is why they can keep up at all before the GTVA exists and the better tech base disseminates to them, and why their ships and weapons are better than their Terran equivalents circa Freespace 2
 * Not entirely correct. The Seth has less primary firepower than the Herc but more missiles, better speed, better agility, and a smaller silhouette. The Horus can run rings around any GTVA fighter. The Amun has ludicrous amounts of armor. The Thoth is just plain frightening. The Anubis sucks because it's a Zerg Rush fighter designed to be produced as cheaply as possible.

The Shivans weren't planning to blow up Capella until they met Admiral Bosch.
The GTVA assumes (reasonably) that if they don't seal off the nodes to Capella, the Shivans will swarm Alliance space and the second Great War will be a conflict they have absolutely no chance of surviving, let alone winning. From a writing perspective, the problem with this is that it makes the loose end of Admiral Bosch anti-climactic; "Uh, sorry, human, we can be friends, but we kinda just glassed every planet your species populated while we were talking. Oops."

Capella is, instead, a stop-gap; the Shivans are willing to spare the human race at least as long as it takes to listen to whatever it is Bosch has to say (Bosch himself thinks the Shivan response to human existence is a misunderstanding, and while that may just be wishful thinking, it could just as likely be conservation of detail and/or Foreshadowing at work) but they don't want any further contact until they can decide what to do with that, and they accomplish this by turning the gateway system between Shivan and Alliance space into a giant roadblock. Assuming there's nothing about an infant nebula in a system that's just been supernova'd to prevent Alliance ships from navigating it, they sure as hell wouldn't want to mess around with it anyway after the Shivans are through making the star explode. That they plan to seal off the jump nodes before the Shivans finish their giant "Keep Out" sign is just coincidence.

The Vasudan found inside the "unmanned" PVS Scarab is actually a civilian maintenance worker.
And you killed him. Bastard.