Attack subs never run on active in the open ocean (nor do boomers).
and what you point out from the article:
...a sounding taken just minutes before the accident did not correlate with the charts that were in use at the time,
Do not necessarily contradict. The other part of the statement about taking the sounding states:
The San Francisco was heading to Australia when it came to periscope depth a little more than 400 miles southwest of Guam to fix its position accurately.
at the point it took the sounding (yes, probably using sonar) it was not "running" but was at periscope depth, likely going very slowly or even at a dead stop for the position fix. (One ping only, Vasily).
The Captain was in error and should have noted the discrepancy between what his official Navy charts said and what his sounding told him. That was where he clearly failed to exercise due caution. However, he relied on the official Navy charts and thus ran into the previously unknown sea mount.
He is guilty of the charges against him and I have never questioned that.
He is at fault, but so is the Navy for having provided him faulty navigational charts and, even more so, for failing to acknowledge that fact in this verdict. They don't admit the problem they won't do anything to fix it. Further, they don't acknowledge the exemplary actions of the Captain and his crew following the collision and, thus, deprive the Navy of this man's skills in crew handling. I wouldn't want him running my boat or teaching how to navigate, but I would want him training my crew for handling emergencies.
You make good points. 'Decision Traps' is a book that should be read. We can expect more accidents if the navy does not fix its charts.