We still have several episodes remaining in season 2.
As far as the fate of the Pegasus goes, I think we'll be seeing them around for a while... but I agree that at some point, the Pegasus will be lost in some sort of battle with the Cylons.
(In the Original Series, the Pegasus was "lost" again, not destroyed. Back in the 1970's, apparently radio hadn't been invented.)
And speaking of the Cylons, now what? Their Resurrection ship has been destroyed, along with the two base stars that were protecting it. Surely it's going to take some time for them to muster new forces to attack the Colonial Fleet, so I predict that now we're going to see a lot of tension between the humans (President Roslin, Baltar, Tom Zarek, etc.).
But it's a good thing that it was Number Six who killed Cain... if Starbuck had done it, there would have been a LOT of tension between the Galactica and the Pegasus.