The main thing that makes me feel an oddness is the
starship combat. Like, I
think it'll work for BSG, but Diaspora is built around a different paradigm of space battle, and harder-sci-fi assumptions are made. Heat management, no fighters, and I'm not sure they even account for FTL jumps in combat (or perhaps that can be simulated by positioning your ship(s) off the +4 or -4 range bands).
Still, the rules they have can probably be made to work easier than trying to roll your own. And the default scenarios of "you're running from someone" or "you're standing and fighting" pretty much covers what happens in BSG. Galactica tries to hold off Cylons long enough to jump out, or they're sending their fighters in to strike at a Cylon weak point, or they're making a stand while their people get off the surface or a damaged civvie ship can be repaired, etc.
My random ideas (some might be mutually exclusive):
1. Fighters could use minion rules and the tethering rules to attach them to named characters.
2. Torpedo attacks and beam defense reskins nicely to incoming Raiders and Flak batteries.
3. Fighter squadrons could simply act as a single-statted entity rather than individual ships or even minions. I mean, generally single hits destroy Vipers and Raiders except for real lucky named characters anyway. No sense tracking damage on single fighters. Galactica's Alert Vipers could be a "ship" to themselves. It would negate the need for scaling as well; a squadron of fighters or Raptors could be assumed to have the punch necessary to damage capships at close range.