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Interesting analysis. It's hard for me to look over Hennesy's words, but this interpretation of them actually make sense. Thank you for sharing. It's just too sad that this doesn't change anything for James and the way he had felt about it, back then as well as later in the years.
I keep thinking about just how much love and affection there is from Admiral Hennessy's side in that final confrontation with James, and how it makes the whole thing all the more devastating.
Had Hennessy responded to the news of James and Thomas' affair with revulsion and anger, it would have been easy, far easier, to cast him aside as a "villain" — both for us as the audience, and also I think, for James.
But earlier in the episode we hear that James considers him to be a father figure and here, right before they walk into that office with Alfred Hamilton waiting for them in it, knowing full well what James has done, he still calls James son:
Good God. You perceive the danger about this to be imagined. I told you when this began to be careful of those people. To be aware of just how sharp and unexpected the knife would be if you discounted that danger. I'd thought you'd heard me, son.
There is no reason for him to do that, not to someone he is about to permanently cast out of his life. Once they walk inside too, Hennesy's lips utter that terrible pronouncement but his expression, his voice is so gentle as he does it. Alfred Hamilton is in the room with them and what James has done is so outside cultural norms, it severely limits what Hennessy can say or do. Without uttering the words, this scene is yet another entry in the show's collection of "this is not what I wanted"s.
In fact, while AH would like to avoid the scandal of his son having a homosexual relationship, I have no doubt there were ways to hang James that would be equally if not more amenable to him that would not cause such scandal, and yet they give him a way out of London without any charges to his person, quite likely because it was the best Hennessy could manage to salvage under the circumstances. And yet still, Hennesy's words:
I would like to defend you. I would like to remind myself that every man has his flaws, his weaknesses that torment him. I would like to help you recover from yours. But not this. It is too profane; it is too loathsome to be dismissed. This is your end.
I keep thinking about what James tells Miranda in s1 re the pardon to go to Boston: "They took everything from us, and then they called me a monster." But who called him a monster? Given how quickly he and Miranda have to leave London after that confrontation in Hennessy's office, not to mention the way the actual affair with Thomas is swept under the rug, I highly doubt he had any more conversations about it except what transpired in Hennesy's office.
It is so much more devastating I think when someone says I love you but what you are is too vile, too profane for me to ever accept. Says I love you but I cannot accept you, and perhaps that is why what James hears Hennesy tell him is that he is a monster.