Jack is hinting that a future with Elizabeth would never happen now. I know the moment was filmed (so were lots of others with James and Weatherby), but most of them were drastically changed both for time contraints, and because they took the film in a different direction.
They basically removed any real hint of Jack being in love with Elizabeth from the original draft of the film to what they decided to keep. I don't know if any of the James/Weatherby scenes or Jack/Elizabeth scenes will be added in, since it contradicts the movie so much.
What I think will be in deleted scenes, if they get to it, would be an extension of the Jack/Beckett scene, James/Elizabeth (depending on the wording), Jack/Will, Will/Beckett/Jones (depending again on wording), Jack/Gibbs at the Brethren Meeting (there was a whole bit of dialogue cut), DJ and Calypso, Will/Elizabeth (pre-wedding), and then an extended Strumpet/Jack/Gibbs scene.
They changed a lot of James and Weatherby scenes to make James less complicit in Weatherby's murder (in the original draft, James finds the body but does nothing), and Weatherby was supposed to attempt to stab the heart (thank god that got cut. I hope it's NOT a deleted scene).
For Jack and Elizabeth, I think they wanted to 'uncomplicate' things. Make Jack angry at her, and also, it's one less story line to follow. The only thing that the deleted J/E 'moments' show is that Elizabeth time and time again shows that she doesn't love Jack. It would have been painful to watch, and it's so much better to just have them be friends rather than have Jack shown to be in some sort of unrequitted love with Elizabeth.
Even in the old drafts of the script, it is obvious that Elizabeth's choice has always been Will. Jack was basically nothing to her...look at that scene that you pointed out, PirateDiva, she didn't even get what Jack would want with her. Romance with Jack is totally NOT on her mind that she's surprised and it appears to be, slightly annoyed with Jack over it. Did you really want to see her reject him again?
Too soap-operaish for me. I'm really happy that the relationship has come full-circle. I was worried for a while that they WOULD make it unrequitted love for Jack, and it totally doesn't fit his character at all.