!!! Spoilers !!!
If I remember right, Pegasus will not be destroyed. I believe Ron Moore commented on this in his pod cast and added something about how destroying the ship would a cheap way out. I hope that RDM and the production stick with that and keep Pegasus as a fixture on the show.
As for the nuke, I think we might see that again in Season 3 involved with the next stop on the long road to earth.
From what I've seen, Ron Moore is taking story elements from the original series and reworking them into new episodes. In many ways, he's retelling the original BSG story in a far better way.
Now story element that hasn't been mined yet is from original Kobol arc on the original series where baltar destroys the pyramid holding the course to earth.
Yay! I found my login to this forum lol.