Yeah, but i think the Pegasus was also in the original series as well. Now as to what happened to it in that show i have no idea (and dont really want to either), but it would be a shame i think.
Either way - there is also practically nobody on board any of the ships, they said most of the pilots and crews etc were down on the ground.
I cant see any way out of this unless they were frendlies (and if they werent why didnt they just nuke them and lauch fighters at the fleet as soon as they arrived?) but then thats what makes it a cliffhanger i suppose.