I've known the story of Port Chicago for years. I was really pleased a couple of years ago when JAG did an episode about clearing the name of one of the "mutineers" as a way to tell the story. And I think they did a pretty good job.
This report is the first time I've heard the alternate "theory" and I normally don't buy into tin foil hat stuff, however, this is pretty consistent information and the bona fides of the main proponent of this theory (a student of Edward Teller - Dr. Strangelove himself) are pretty impressive.
I don't buy it, anymore than I buy the "philadelphia experiment" crap, but I can't dismiss it the way I can other such stories. Particularly not with current evidence of higher than background radiation in an area consistent with the fall out from a low yield test device and the high incidence of cancers in the same area. I lived in the Bay Area for about 5 years and remember lots of speculation about the high cancer rates in that area.