I think this is just a philosophical disagreement, which is cool.
That's why I said, as far as the show is concerned, based in truth or not, she was a real person inside the framework.
So whether or not we agree with her, Jemma is reacting to Fitz killing a human being, and Fitz will likely be reacting to himself doing that too (if he gets his memories back).
Also keep in mind, Fitz thinks this is all real still. So even if it WERE just a program of a person, he shot her thinking she was a real human being. So whether or not he actually did, he made the decision to kill a human being. In the end, that's a huge deal.