I still stand by my theory that the Shivans obvious (or maybe not-so-obvious) screw-up in blowing a lot of themselves up in a heated inferno of star matter and flame was all of because of Bosch's influence in the matter... ETAK, communication with the Shivans, Bosch messes with Shivan communications to screw up the Shivan attack on GTVA space, yadda yadda yadda...
It could have simply been that Bosch wasn't as evil as everyone thought--he may have saved humanity by having the Shivans nuke Capella, but by that same move, divert 80+ Shivan juggernauts from the attack on the Vega or Epsilon Pegasi node, which surely would have:
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- Utterly destroyed the GTVA fleet
- Opened the GTVA core systems to invasion
So Bosch did a lot of good--stopped the Shivans, deepfried dozens of Shivan juggernauts, and gave us a pretty little end cutscene for FS2.
So, therefore, the Shivans'
usual tactics, as elaborated on by Kara above, of blasting through fleets and
then destroying star systems was stopped by one madman with communications tech. Bosch wasn't bad, eh?

Actually, now that I think about it, couldn't destroying a star simply be the Shivan method of making their own victory
really clear to their enemies? Maybe when they destroyed the Ancients in one sector of the galaxy, they pulled a Capella on one of the Ancients' more important star systems in that region, and then moved on to destroy the Ancients in another area, simply as a way to show their enemies that "You've gone too far, and now we're going to make you
really pay for it"? Bosch might have simply told the Shivans that the GTVA had "learned its lesson", and therefore told them to give to give their final word on the matter--thereby nuking Capella.
I guess it would somewhat make sense that the majority of the Shivan fleet would get obliterated here--maybe when the Shivan were finished with the GTVA, they would finally put an end to the bloodshed by simply killing everyone in the system, including themselves? This still doesn't explain the juggernauts warping out at the end, however; although, they could have simply been going off to punish a less powerful trespasser...