Nice post, and I'm all but certain it was intentional on Hitchcock's part. As you said yourself, Hitchcock was a perfectionist; there's scarcely a frame in any of his films that isn't the way it is by design. I think other than Hitchcock only Kubrick was so much of an obsessive perfectionist in the history of film directing.

I don't know about you, but it kind of sounds like a story climax isn't the only kind of climax happening there!
Way late reply, but totally agreed. I remember being very struck by this scene when I first saw the film many years ago. There seemed to be no mistaking, IMO, what exactly Hitchcock was getting at there. The way he holds her, the positions of their bodies as they struggle, and the dialogue all work together to pretty obviously suggest a metaphor for a violent sexual encounter. And I think Cotten and Wright were both well aware of this and played it to hint at just that, probably with Hitchcock's urging. In fact, I find that the incest subtext gets very much stronger in the latter half of the film altogether, and would seem to be almost unmistakable and quite deliberate.
I'm betting there were more than a few audience members back in 1943 who picked up on the underlying intent of that sequence as well.

I have seen this film more than a dozen times and honestly I never saw that specific scene in the view you just pointed out, Kikiteka. Seriously, how odd, I was totally oblivious to the obvious undertones here. And now, it's not that hard to believe actually.
I mean, I knew there were hints dropped here and there about Unclie Charlie's true feelings for Charlotte (his niece!), but the writing in this scene really hits the nail on the head! I know Hitch battled with these sort of demons during his lifetime, and it came out ugly with Tippi Hedren during The Birds, but he sure did sneak into this filmI guess it took to actually reading the words than hearing it.
Back then they had more constraints with ratings, what you could and couldn't say and the implications of the words. But I guess they had ways of still getting the message across to viewer.

Ah That makes
sense actually. Sure, it's a bit gross, but the slightly disconcerting subtext is all through the movie. I always assumed it was just my own sick little mind that thought that the dialogue in that scene was kind of questionable. So basically the reason Charles doesn't strangle her first is because Hitch was a big pervert. Gotcha.

Well, there's that, and there's the alternate analysis of what's happening in that scene. It requires having a bit of a dirty mind. I would just like to say that I did not come up with this, so don't blame my dirty mind!
They're on the train tracks, he's flung the door open and he's getting ready to throw her off the tracks.
Uncle Charlie
: I've got to do this, Charlie, so long as you know what you do about me.
He twists her around as she grapples with him. He repeatedly lifts her so that her feet keep leaving the floor. She stares at the tracks, and we see two parallel railway tracks blend into one. He says
Uncle Charlie
:Not yet, Charlie, let it get a little faster. Just a little faster. Faster! Now!
Screaming train whistles, she reverses position and pushes him off.
I don't know about you, but it kind of sounds like a story climax isn't the only kind of climax happening there!
Like I said, I'm not saying that was intentional, but it sure does put that scene in a different light doesn't it! Yes, Hitchcock was a perfectionist, and yes, he was interested in Freudian psychology, but maybe that's giving a scene way more meaning that it was ever meant to have. So, intentional or not? You be the judge.