So, when I first heard about the whole Chiana is Karen Shaw thing, I laughed in utter delight.
There's a twisted circle going on -- Chiana sleeps with John, therefore, when John meets Chiana, he feels inexplicably close to her and ends up saving her life. He treats her like a person and is mostly just damn cool. Therefore, she falls in love with him (she totally does). Therefore, she sleeps with him when she has the chance, when he's young. So, because she wants him, he trusts her and because he trusts her, she wants him.
I wonder how the whole thing would have turned out without Aeryn's involvement, because they have such an interesting relationship. Though perhaps it wouldn't be as interesting were Aeryn not there. Because John comes to love Chiana and he's definitely sexually attracted to her, but he's In Love with Aeryn, capital letters. But since I don't believe in that one One True Love, Now and Forever, Souls Connecting Across the Great Divide, I wonder what might have happened if he'd met (well, known that he'd met) Chiana first.
Hell, just Chiana's presence was a disruption. I'm sure that someone said (on a commentary?) that originally she was just supposed to be a one-episode character, but they liked her so much that they brought her on permanently. Now, the John/Aeryn juggernaut was already in motion at that time (in the very next episode, they have sex, I believe), but Chiana has a definite effect on everyone. She adds a certain unstability to the whole enterprise.
Recently re-watched Taking the Stone, which I adore, and Chiana and John's relationship is shown in all its dysfunctional glory there. John's already started going crazy, as we find out in Crackers Don't Matter, but even taking that into account, he's so damn intense with Chi here. "No matter what you want, you cannot want to die." Fully willing to override her stated wishes and break his previously given word if it'll just keep her alive.
Because I think that part of him does want to treat her as a kid sister (because he loves Aeryn, he really does), but that sexual energy crackles between them (and his body, as we find out in Kansas, knows her already), and his touches on her aren't those of a sibling.
None of John's relationships in the UT are without complications.