Morgan followed her directives perfectly though
The guy interviewing her asked her to "demonstrate what you would do if I told you I was going to terminate you." If he told her he was going to terminate her, she would kill him and try to escape (as would anyone in that situation). So she demonstrated killing him and escaping. She was actually just doing exactly what he said.
When it happened, I thought they were going to this idea as some kind of "twist" towards the end, where it's revealed that she actually had no emotion and the entire escape was just the AI following his command.