What is the best outcome for
It's hard to judge given there aren't any serious consequences yet. And for the sake of... "optimality", you should probably kill the Witch to have one more sex scene. But I'd gladly discuss our logic/morality in this.
I can't imagine a world where killing all the witches would solve the problem of transdimensional travel or whatever happend to the MC. In a few generations someone would eventually find some information, dig into it and the cycle repeats. That's why I hope that with our help, the Witch would understand the topic and hopefully not repeat her mistakes. Don't get me wrong, I don't trust that she is (or they are?) doing it out of curiosity/good will and might even have some bad idea of bringing some evil unto the world, but what better option do we have other than continuing on the only path ahead? Pretend this doesn't concern us? I dunno man.
The problem is, who do we trust? Nakaan? To me, after playing every possible outcome, she seems like a simple person with straightforward goals. Or a very good liar (unlikely imo). Neither of those options exclude the possibility of her being a pawn in someone else's game. I mean, someone could try to kill all the other witches to monopolize this new power or something, it might have major consequences later on. But all she offers is being "a friend" and eventually using that argument to get some help from an assasin later down the line. I'm not saying no, but...
As for the Witch, I haven't played in a while, but to me she doesn't have much controversy. She seems like a rookie in some... "mischievous" organization. She did help us, but I didn't really feel like she cares too much about the MC. I know your own safety is important, but how easily she kills MC if we pick bad options during the first meeting and how she ignores us if we tell her she's being hunted... Something's not right. And don't get me wrong, I'm not saying she's bad per say, just that we aren't of importance to her and I kind of don't trust organizations that treat sentinent lives as "expendable".
What's my conclusion? Witch being alive might be of use later. No matter if you tell her or not about the assassination attempt. Honestly, if I didn't know she'd dissapear, I'd report it to her. Anyway, she'll remember that she's in your debt, becouse she dragged you into this world, or even that she owes you her life, becouse you stopped the assassination attempt. Even if not, she's still an interesting lead that might get us somewhere interesting. While Nakaan can be reasoned with. She might suffer some consequences from her boss, which will never outweight the (unreliable) ally candidate Witch is and I don't think she'd rat us out, I mean, who would care for such a weak excuse as "some guy stopped me"? Also, I'd imagine if you didn't rape her, you could meet her in a year or so and have a friendly talk. You could have killed her and be done with it all, but you spared her life. She should still feel some sort of gratitude.