I doubt Galatica and Pegasus will start actually fighting, because the writers aren't that stupid. Pegasus would wipe out Galatica, thus ending the series. Or some stupid equalizer will be introduced. In any case, you can't have the humans fighting (well fighting yes, killing no) each other, it goes against the spirit of the show.
One more thing. If I remember correctly, the new Vipers (the sleek grey-blue ones) are susceptible to Cylon electronic attacks, as a whole squad was wiped out in the miniseries. How come they're still in use? Wouldn't they be next to useless?