She is in alot of denial about the whole situation..she thinks that she SHOULD want Will but her heart is telling her that she wants Jack...Sadly at the moment she listenes to her brain instead of her heart..She forces herself to be with Will by chaining Jack up..even if Will is not who she really wants.
It's still only the middle of the trilogy..So far the characters aren't supposed to really accept what they want just yet....there are hints in both movies showing the audience what they TRULY want..like the ones in movie 1 where it's clear that Liz is obssesed with pirates since she was a child. And all the hints in movie 2 point to it aswell...i
The hints in movie 2 are pretty much pointing to Liz choosing Jack and a life or piracy...