I think that was a bad move, to make the wish responsible for their relationship and their interactions. The wish was never about that, it was to protect her life from the djinn, not to bind her physical to him or even influence their behaviour to each other.
As i said already here or in other threads the wish isn't even mentioned later on in the books anymore, because the "effect" of the wish was never to influence their relationship. It was a typical fate thing, which is quite usual in the Witcher universe.
Maybe the easiest way to understand that fate thing is, if you take Ciri into consideration:
Ciri was Geralt's fated child and so is Yennefer his fated woman, both times by his doings and only by his doings.
If you agree in the Last Wish that nothing has changed, it just confirms that the wish never influenced it, it is "lore-friendly", but if you disagree, well
About confronting her, i thought the quest in the Garden of Freya was already quite fiery. Depending on what you choose to say, you can either doubt everything she does, resulting in a kinda pissed off Yennefer, or trust her and go with the flow.
E.g. you can try to lecture her about black magic and she doesn't like it at all, she isn't a child, as if she didn't know already that it is risky, but it is for the sake of Ciri and she can't understand that Geralt is hesitating for her sake, even though i would like to remind you how many people you already killed up to this point in this game, just saying.
At the end of this quest, she asks you for a favor (which begins The Last Wish). If you tell her to meet her there asap, she is really thankful that you helped her so far
"Geralt, you know me. I'm rare to praise, but when i do, it is sincere."
But if you tell her that you still have other things to do, she says
"Well, if you must, you must. I shall wait for you in Larvik for a time. If you don't make it, we'll meet in Vizima."
She asks him for help, not command it. She would even accept that you don't help her.
You can also tell her that you won't report anything to Emhyr, what does she say to that?
"Fine...I can't force you."
Or at the mourning ceremony you can assure her to not drink any alcohol to have a clear mind, but you can still drink until you are quite drunk anyway and she gets angry with you because of that.
I think CDPR tried to reflect their relationship from the books, showing a quick and brief iteration of it in the games with the "Last Wish" as turning point.