Have you ever slept in a berthing compartment aboard a naval ship? You assumed the clock started ticking at the moment of collision, as if it were a shotgun start to a foot race.
First of all, it's fairly dark in a berthing area at night. A few red lights are lit, and perhaps a light or two in the head. Most sailors sleep in their underwear--briefs, boxers and a tee shirt. Their boots are usually nearby, and perhaps they have a set of utilities that they can pull on relatively quickly.
No one knows precisely what happened to the berthing area where the sailors were trapped, though it's very likely that all of sleeping sailors were jostled awake in some form. Very likely, many were thrown from their racks, and were likely disoriented, initially. Remember, it was already dark, and now you introduce the possibility of flooding into the berthing compartment.
For those that can move on their own, their instinct will be to move to the ladders leading out of their berthing, maybe grabbing whoever else they can on the way. Despite the motivation to get out of that compartment, a queue would inevitably form--perhaps some sailors are pushing into others with urgency--depending on how quickly water poured in.
It's quite possible that many of the deceased sailors were injured immediately during the collision, and couldn't move on their own. They may have been knocked unconscious, or perhaps even killed upon impact.
So your minimal time of ONE MINUTE, while generous-sounding, still doesn't give them much time to get out of their berthing area, not considering the environment and the circumstances.
As for the CO, he will undoubtedly be blamed and will become the historical fall-guy, as skippers always do. But people should realize that even skippers need sleep, and require to be wakened when their presence is needed--such as in an emergency. Given that the Captain was injured and trapped in his cabin during the collision, we know that didn't occur, at least not in a timely enough way.
I have several years sleeper in the berthing compartments of both DDG and LHA.
Your points are valid.
These guys were likely injured upon initial impact. Some may even have washed out the hole in the side of the ship.