For the muscle-ups, the fact that they jumped into it isn't that big of a deal. I mean, doing a muscle-up -- especially for a woman -- is impressive, period. CrossFitters do sometimes use jumping pull-ups for people who can't do regular pull-ups, and, trust me, 50 jumping pull-ups will burn you out... even if you do consider it cheating or shitty form. Try it and see.
Same thing with the 50 bodyweight squats -- I thought that they looked easy until I tried it. Even now, I'll use 50 bodyweight squats as a warm-up or to burn out at the end of my workout. It's good stuff -- you should give it a try. Of course, I would never recommend (as CF kind of does) to do bodyweight squats exclusively.
I'm not sure what the medicine ball is all about either -- you can do bodyweight squats perfectly fine without them. Maybe it's just to tell them that they went down far enough?