Interesting document, and a very unique take on the Shivans and their purposes.
However, I think it would be unfair to discount the "bigger, badder race" idea out of hand. I always imagined the Shivans as like puppets. They didn't go say "Hey, look, a bunch of squishy people with two legs. Let's kill them!", they were ordered to exterminate the Terrans and Vasudans. And being puppets, they must have a puppet master somewhere. Imagine, if you will, an extremely old (on the order of tens or hundreds of thousands of years), extremely advanced civilization that is obsessed with being top dog in the FreeSpace universe. They do this not by continually advancing their technology, but by creating the Shivans to destroy any subspace-capable race before they can become powerful enough to challenge the puppet masters so they can wallow in stasis and decadence without having to worry about any competitors. The Shivans' technology was provided to them by the puppet masters. They were supplied with just enough power to obliterate any subspace-faring race in its early years, but not enough to pose a risk of getting out of hand. They have probably sent the Shivans and their Lucifer-class ship to devastate dozens of civilizations, and every time they have succeeded.
But the Terrans and Vasudans are an exception. They have thrown a monkey wrench in the puppet masters' strategy by adapting and advancing quickly enough to fight back Shivan invasion, something unprecedented in the FreeSpace universe. At first the puppet masters thought the Shivans might have been a bit late to the party, so they gave them some better hardware, and sent them to go kill bipedal lifeforms again. But when the Shivans listened in on Bosch's ETAK transmissions, it completely threw them for a loop. Keep in mind that, even when Bosch is communicating with Shivans, Shivans are still aggressive and vicious creatures and your average NTF marine would probably react poorly to a horde of Shivans pouring out of the airlock. The Shivans probably regarded the lesser members of the crew as beneath their consideration and slaughtered them casually, while sparing the senior crew and Bosch himself. I do not think the Shivans came to kill or torment Bosch, but to investigate him and learn about Terrans. I think what they found out surprised them completely. How they reacted, one can only guess. Maybe blowing up Capella to create that jump node was so that they could go somewhere far, far away, where the puppet masters or vengeful Terrans and Vasudans could not follow, somewhere where they could repent. Maybe they did it to bring Bosch to the puppet masters (in which case Bosch would soon end up very, very dead).
Whatever happened, there's likely a new invasion in store for the GTVA, and it will likely come from the puppet masters themselves. As lazy and corrupt as they are, they really don't want us sticking around and have twice tried to eradicate us indirectly. The Shivans are the symptom of the disease that is this decadent, bitter, and completely amoral race. The methodical and detached way in which the Shivans go about their deadly trade and their seeming disdain for territory or resources bear the hallmarks of a tool to accomplish the task of destroying other civilizations, a tool that must have a wielder.
The "bigger problem" is the puppet masters, who have maintained their dominance by sending the Shivans to crush any upstarts without having to personally involve themselves in something as dirty and inconvenient as warfare. But now the Shivans have proven to be ineffective at stopping the GTVA, and the puppet masters will have to resort to more drastic measures. The GTVA better get on its game, and fast.