These people just have a problem with their own erroneous idea of a strong-willed woman. Aya fans have once again hoped that this character would never go down like Laura, not only because they completely misunderstand Aya as a person, but because they have some weird idea that Aya can easily handle a situation like this. In other words, Aya fans imagine that she's some kind of superhuman because that's the only thing they got from this character in the original game.
By the way, the same completely stale debate has been going on for decades with Rei vs Asuka in Neon Genesis Evangelion. Aya and Asuka fanatics are the same kind of people who have infinitely high expectations of a strong woman that they might find personal redemption in her. It's just as ridiculous as it sounds. Maybe to compensate for their own helplessness or because they would love to be protected by a competent woman, either way they both have way too high emotional attachments and high expectations, and complain about the writing when the cognitive dissonance kicks in and gives them a reality check.