... Wait, why is Balamb Garden getting destroyed a full-on bad ending instead of a tragic doomed 'hometown' event?
All your characters except maybe the ones at the missile base are still around and hresave been operating semi-independently of Garden orders for a bit now anyway, all the Garden getting blown up does is kill off background NPCs and remove the people assigning missions, giving rankings, and sending money to Squall's account every so often.
I mean, yeah, it's a tragic waste of human life, but the main cast has kinda been cut off from Balamb ever since it turned out their contract with the Timber Owls had no end date and they weren't going to be able to just leave. Why does their journey's success or failure hinge on the upper management who only care to send the occasional check surviving?
Edit: Like, are we really sure "Oh no, the people randomly docking your pay for doing things that tarnish the reputation of their child soldier mercenary academies reliant on memory-loss-inducing giant monsters for powerups are dead" is a Bad ending? Is all this just because the programmers refused to make an alternative to the SeeD Rank mechanics for how your party funds their misadventures?