She doesn't want to hurt Will, but damn it, sometimes this is what she needs. Will is sweet, for all that he's embracing his pirate-ness these days, and sometimes what Elizabeth really wants is Captain Jack Sparrow, all swagger and rum, who knows what he wants and goes for it without asking "Is this alright?" or "Should I do something else?" - who grabs her ungently and leaves bruises on her thighs and fucks her hard and fast and perfectly without being asked at all.
Because that is fun, but even more fun is not feeling guilty about getting a bit of her own back, pinning him down when he least expects it and riding him slow and messy until the unflappable Captain Jack is thoroughly, utterly flapped, until he's whimpering and begging and trying to pull rank on her, because then she can lean down to remind him that yes, he may be a captain - but she is a pirate king. Which reminder, for reasons neither of them cares to explore, tends to make him buck up against her and come hard enough to black out. Which makes her feel very powerful, and very happy, and also just about ready to come herself.
What happens on shipboard stays on shipboard, right? Because what a ship is, is freedom - and Elizabeth is enjoying her freedom to the hilt.