“Certainly, we are addressing a perceived lack of fitness among recruits,” O’Connor says. “People are doing too much, too soon, too fast. Participants [in high-intensity programs] need baseline strength and flexibility, and they simply aren’t prepared.”
I don't see anything knee-jerk about that. That is pretty sound thinking, to me. You take some 18 year old that has been sitting on a couch, watching TV and drinking Pepsi for the last 18 years (yes, I have seen parents giving their new-born babies soda in their bottle) and throw them into a CrossFit-type workout under military leadership (which means 2-3 Drill Instructors yelling at up to 100 people at a time to do more, faster, NOW!!!) and I can see a lot of injuries and probably a few deaths.
Ignoring the basic physical requirements for now: a lot of CrossFit WODs really require specialized training and a much more "1 on 1" instructional approach that the military just can't give in Basic. I think something post-basic (Marine Combat Training, SpecFor training, Infantry School, et cetera) would likely be a more appropriate place and time for high intensity training.
Basic is a good place to get basic fitness.