None can understand the mind of a djinn, I guess, or to be pedantic about it, know what specific rules a specific writer has applied to a specific instance of a djinn. But if Geralt's wish is that his and Yennefer's destiny be bound together, the djinn would have to kill both of them, and to fight Geralt would be no easy task, possibly ending in failure and the djinn's recapture. (Remember, Yennefer has been keeping Geralt away from her attempt to recapture the djinn.) Prudently, the djinn "gets the hell out of Dodge".
Geralt was temporarily the djinn's master when he first held the lid, so the djinn probably doesn't want to kill him.
It may be as @Guy N'wah says, and the djinn based its decision out of fear(or wisdom) of fighting Geralt, or possibly, there is an unwritten rule that the djinn cannot harm a former master/wisher. Because who in their right mind would then set a djinn free if there was a certainty of death immediately after the last wish? I believe the three wishes of the djinn/genie myth is meant as a reward for setting it free, ergo the djinn leaves the former master alone, grateful as its freedom is worth more than the petty three wishes of man. Possibly it goes after the one putting it in its prison in the first place. :laughing:
Well, yeah. If you're disturbed by Yennefer's character, it's a sign that you're getting the point. In spite of all that, Geralt has seen something in her that has changed him. And there is no accounting for where the "thunderbolt" strikes.
