Thermodyne: "So if we take the 39K number, what would the effects of surviving a nuclear war and several close proximity fission detonations have on them?"
From the mini-series I got the impression that most of the survivors were already off-planet during the initial Cylon attack. The ones Boomer picked up from Caprica were at some distance from the nearest blast and apparently made it off before the fallout started dropping. As I recall, Galactica herself took a nuke (near miss?) at some point in the series, but since the electronics came through OK, the ship must be well-shielded from radiation.
As for Baltar's nuke, the FX guys produced a pretty good simulation of an atmospheric blast engulfing nearby ships, but that's probably not what would happen in RL. Extrapolating from what I've read, I think the warhead would probably vaporize part of the Cloud 9 ship. Within this "atmosphere" the nuke would probably produce the usual radiative and blast effects, but the fireball would be no bigger than the ship and would dissipate rapidly at greater distances. I suspect the nearby ships would experience more damage from fragments and radiation than from blast. No doubt the fleet's civilian ships carry shielding adequate to protect against solar flares; I have no idea if this would be enough to protect against a nuke at a distance of several miles. Anyone on the ground, of course, would probably see some nice auroras in the following days.
Actually, it occurred to me while writing this that the fleet might not maintain a cluster formation while orbiting New Caprica. Ships closer to the planet than the Cloud 9 ship would effectively be in a lower orbit and gradually pull ahead; ships farther out would fall behind. Ships separated laterally would actually be in crossing orbits. My guess is that the fleet would form line, orbiting the planet like a string of pearls. In that case, Baltar's gift to #6 might not take out more than one ship.
Thermodyne: "I hope this is just a tease for next season and not a cost cutting measure."
I suspect the writers were trying to deliver a real shock to the viewers: fast-forward a year and then leave our heroes in an apparently hopeless position (again). If so, it worked; I was screaming "Jump, you idiots! Jump!" at the TV as soon as the Cylons showed up again.
I predict the fleet will stage a heroic (and hopefully plausible) rescue operation using Sharon's talents (again) and plucky Starbuck's military skills on the ground, before resuming the trek to Earth.