I originally worshipped the Will and Elizabeth pairing, but the second movie suddenly converted me and now, I'm rooting up for Jack and Elizabeth. They just look good together (although Will and Elizabeth looks good as well) and I really fell in love with their special moments at the movie, especially with 'the kiss'. I am really enlightened with all of your accounts, but I would like to still see Will and Elizabeth together despite that and a non-biased third movie would be great.
Will is a laid-back type of person so it's no surprise that he didn't interfere with Elizabeth and Jack kissing. And besides, if he just followed his heart and suddenly jumped back into the ship, taking out his sword and pointing it at Jack (or at Jack and Elizabeth, for instance), wouldn't it be an unintelligent move since it would cause a great scandal? The crew and other people would be aware of the fact that Elizabeth was having an affair with Jack and would cause great shame to Will since he's the one who was cheated on. And with Elizabeth's denials with regards to her real feelings for Jack (if ever there are any), she would be disgraced too (well, she's not even thinking about it before she kissed Jack). I supposed Will isn't impulsive as Elizabeth for him to do such thing (to just interfere with the kissing 'couple'😉. He chose to do what his brain told him to. Yes, he did sat down and frowned all the way, contemplating about the fact that his fiancee cheated on him when he believed that they are in love with each other, but the thought of that never left his mind. I guess he's planning on confronting Elizabeth privately afterwards without having to discuss the whole situation to everyone else and then Elizabeth (with her usual denials and lies), will apologize to Will and state her defenses. Of course Will isn't too happy about that, and will have second thoughts about continuing his marriage to Elizabeth. Yeah, he's absolutely hurt by Elizabeth's actions, but we can't deny the fact that he really loved her so much, although he isn't that good in expressing it. Not all are good in expressing their love and other emotions. And we can't really say that he doesn't love Elizabeth 100% just because they don't kiss often, hug often, flirt with each other often, say "I love you" to each other often. Just a simple act and motivation of risking his life for her just answers every single doubt.