I realize that some have tried to make lame arguments about her position in the water, and other completely nonsensical arguments, but, for a short while in the early 90's, I spent some time working with a Captain who was charged with unclassifying some of the details of the Scorpion and Thresher sinkings, in response to Soviet claims at the time that they wanted U.S. help in recovering one of their sunken submarines (I don't recall which). The basis of our analysis was to prove that we had two nuclear submarines lost, one with nuclear weapons on board (the Scorpion, that was one of the things that was declassified, press release here, some decent info here), and that the Russian argument that their submarine posed an environmental hazard and should be salvaged was B.S., since we had then almost 30 years of experience monitoring the wreckage sites of these two submarines.
Anyway, while the Board of Inquiry could not definitively say what sunk Scorpion, the most likely scenario was a hot running torpedo, that either exploded in the tube, or that hit her soon after being released.
I feel for for those loved ones who lost family members and have never been able to get a definitive answer for what happened in May 1968. Hell, we all served on these boats, we all knew what the dangers were. I think I feared a MK48 hot run more than any nuclear accident or attack, it was probably much more likely (except for a battery fire), but that is what happened in the Scorpion's case. I agree with Admiral Trost:
“I think it’s totally unlikely. Nonsense. Let the families have some peace, instead of dragging it out with new speculation and books and queries of the families.”
Update (5/19/08): There are some good comments over at Neptunus Lex's blog on this, go read them (H/T: The Subreport).