The way we dealt with it in TI is that the star disrupted Subspace itself when it was destroyed, it didn't change any of the established and stable jump-nodes, but because (we assume) there was some sort of subspace portal opened by the Shivans when it was destroyed, it's theoretically possible that the explosion ripped open some new 'exits', those exits could, because of the nature of subspace, lead practically anywhere. Of course, this science is based purely on what little information we have on Subspace, but I've always been of the opinion you can do what you want to the 'universe' in FS2 as long as you leave the canon stuff alone.
Of course, I've always wondered whether the only fault of the GTVA was to get between the Shivans and their actual target, they may have been going home, or they may have been fighting another race entirely, and needed to go through GTVA space to get to somewhere suitable for opening a jump gate. Let's face it 80 Juggernauts could have obliterated the GTVA in days, instead they simply flew in, blew up a star and vanished, that sounds like 'just passing through' to me.