I think Jack's motivations are to originally, take Elizabeth. I seriously think Jack becomes the number one bastard in the movie, if only briefly, by betraying the pirates to Beckett.
Will mucks up his plans somewhat, and in the course of talking to Will, Jack realizes how much he's been hurting Will AND Elizabeth, and he seems to get it that he could maybe help Will out.
However, Jack being Jack, has to make sure that all his bases are covered. He has to get rid of Will, because if the plan goes to hell, he can put the blame somewhere else. Who would doubt him if he told them that Will betrayed them all to Beckett?
At any rate, by the time the council is over, Jack has made his decision; he will fight for the pirates. It explains why Will is still uncertain with Jack, plus by leaving Will in the dark, it makes his reactions more genuine.
So to answer your concern, I think that Jack had come to terms with Elizabeth and Will loving each other and wanting to be together, but fate steps in once again when Will is mortally wounded, and Jack makes the choice to help save Will, because at least his friends would have some small chance of happiness.
Being captain of the Dutchman sunders Will from Elizabeth for 10 years at a time; being dead would seperate Will from Elizabeth for all time. Plus, I don't think Jack wants Will to die, so the motivation isn't purely for the happiness of Will and Elizabeth. In Will, Jack has found a foil and if he can allow it to develop, a friend and great ally. If Jack's character has grown at all, then he won't want to lose that friendship if he can help it.
Just my thoughts. I'm tired too, so this is probably incoherent.