As Saito S
pointed out there is no analogue to raising shieds in present warships (I thought about mentioning that, but was just too damned lazy!
), so your example breaks down at that point.
It really doesn't. Flooding the tubes of a ship preparatory for launch is basically a detectible defensive measure that the other sub can hear. You actually don't have to plot a firing solution or have any intent to fire, it can quite easily be just a readiness measure... Not unlike "shields" in the ST universe*. There are no perfect analogies obviously, but the analogy needn't be exact for the psychological point to come across.
And I take it it's coming across, yes? It would in fact be really spectacularly unlikely for an American sub commander to assume even in a peculiar situation that one of his own ships is the enemy and to prepare accordingly, right?
(* If real-world sub commanders could double their armor at the push of a button, you can bet that with that more perfect parallel, that too would be read by other ships as an indicator of intention to do battle. The thing about defensive measures is that they're also potentially offensive measures.)
But even it there is any residual psychological resistance, that presumably is precisely why GO 12 exists.
I'm not talking about "residual psychological resistance." I'm talking about its being a basic pyschological component of your average navy -- and Starfleet is essentially a Space Navy -- to have an extremely strong inhibition against firing on your own ships or assuming they will fire on you.