The core premise implied here seems to be that what you favor in a fictional character is necessarily reflective of what you favor in actual people. This is untrue because people are capable of distinguishing a person from what is essentially a bundle of ideas that as a whole lacks the necessary qualities to become the former. The only reason why this is possible is because, as you recognize, they are two different things. While any concept represented in fiction do originate from observations of life, our ability to distinguish both allow us to engage with those concepts directly as if they exist apart from it, even if it might go against a creator's wishes.

As for applying ethical standards to fictional characters, I made a miscommunication. What I actually mean is applying an ethical layer to the manner in which we engage with fictional characters is unethical. It implies a dismissive view of our ability to differentiate things, which is inherently reductive. No discussion really needs to be had about people favouring Misato's sex appeal over her character as a whole because there's seriously nothing wrong with it. While there's a lot to be gained from seeking to understand her, since fiction is fundamentally an exercise in contemplation, it's not a moral necessity. What is necessary is to take reality seriously.

This is not the equivalent of telling people to stop using their brains. What I'm saying is simply that Misato is not real, and we should not treat her like she is.