@soupcrackers
I get your point, but I view MC slightly different. It is only mentioned here, but If she really got emotional over characters in the book it would be like meeting someone you knew before who changed a bit (Ilea) - you like the person so you still side with her (though she is no longer as she used to). I met many people behaving like this in real life. I also tend to give credit to someone who is no longer great, because we were close to each other in the past (It takes time before I will get used to the change in personality).
Also when it comes to Ignis, it is so hard to say what kind of character he is. His actions, thoughts and words don't match neither villain nor good guy to me. (but that's probably why I find this story so interesting). MC is so prejudiced when it comes to him, cause there are high chances that he will get her and her loved ones dead. At this point of the story, it is still highly possible. It is pretty nicely shown that she is frightened when it comes to Ignis - this won't let her give him proper character evaluation (not too mention evaluation of his motivation behind actions).
So I think MC is not the brightest kid I've ever seen, but I can follow the logic of her actions (which are highly influenced by emotions and knowledge of possible outcomes). She starts realizing that story is not exactly as she knows and that people are not just characters, but she is extremely defensive (which backfires), so she tries to avoid anything which could go as in the novel (she is a bit too obsessed with the novel story, but I think most of this "reincarnated in book" stories go like this. And I think that's also quite reasonable that you believe the outcome to be the same unless you manage to make some drastic changes to the plot and it won't return to the original through other means).
And one more thing - alternative with killing original ML and FL is interesting, but not possible in my opinion, given that only person which can make changes for this to happen is our MC, who is not capable of intentionally bringing someone good to death. (I mean she is portrayed as a really good person, so killing doesn't seem as something she could bear to do)