it was a really poor decision to have her run in the NCAA 5000 indoor final and that could not have made her family happy. It may not have been the reason but it could have been a factor.
You are implying that her coach pushed her to run. Yet other people have reported that it was opposite. That Natalie Cook was the one who pushed her coach to allow her to run.
You make some good points about altitude vs. sea level effects. Overtraining is a term that can be used several ways. Here I was talking about training at a high volume or intensity level or both to the point where runners are so fatigued that they are seeing diminishing performances and possibly injuries, whereas a runner like Cook will not get to either high volume (of actual running) or both volume and intensity and so will not be overtired in the same way. She's able to hit her workouts, I am sure, because she's fresh. I was reminded of what a difference that makes the other day when it was cooler and because of a low level cold I had taken a couple of days at 7 miles or under and I felt like a new man out on my morning run. Cook was hitting really good paces at her best as a fresh athlete, but the pounding of her feet on road or track gets her injured. I never found myself anywhere near as tired at altitude with the same mileage as in hot and humid weather in Florida.