Nettie will get hostile after failing the checks. If you are good you will not want to kill her, because she has a point. Talking to her also makes sense, she is the apprentice, she has additional information and might be able to help since she also studied the tadpole. There might have been recent conclusions she came to. It is logical to talk to her, if you had a disease and there was only a nurse nearby, who knows where the doctor is, you'd ask her for info as well.
Now yeah you could not knock her out, but I never got knocking out to work, the victims just died. It might only work from stealth and out of combat, I do not know, and there is noone telling you how it works. Stealing would be the optimal option, but not everyone's cup of tea.
You could use the cauldron, but there is an additional issue: When you press alt it is not highlighted, so you might totally miss it. You might as well miss the book that gives you the recipe for the antidote. Also there are roleplay reasons why you just do not rummage around in people's documents when the person is around. The game simply does not give you enough hints to make educated choices, that is why many players will just endlessly reload until they get the option they wanted, however improbable that is. That is an UI problem and a game design problem. The game funnels you into one option, partly because they created the encounter this way, partly because the game is lacking an actual relevant tutorial and partly because the UI is pisspoor and partly because their dialogue writing and conversation system is at times suboptimal.
I agree that Larian didn't write this one out well. There should be a better opportunity to back out without triggering a fight. You should be able to refuse the 'treatment' and leave without a fight (or with only one fairly easy check). But once you get 'treated' I'm fine with how things play out.
