You could just do nothing about it. I'm fairly certain no one gave a damn until you pointed it out. Gloss/ignore the event and move on with your regularily scheduled roleplay.
...
Well, whatever would happen would need to happen with Albini and Tami as far as Yamatai is concerned. Kenichi's Star is also affected, though this is something more tied to independant plots, if I'm not mistaken.
Map-wise, you could look into shifting the position of the Ayame nebula as it gets pushed/blunts the shockwave with its mass.
Honestly? I'm not sure anything can be done about it but have people batten the hatches and try to weather the natural disaster as best as they are able. Space is vast, wondrous and dangerous, and dwarfs even mighty Yamatai.
This is the reason why people should be reticent to blowing up stars: it catches up with you eventually. It's rich motivation to not screw around with that kind of warfare. I think this is important.
The Kohana supernova isn't the only concern. There's also the Taiie supernova, and the swath of destroyed systems Uesu left in the wake of his exodus too.