Their food sources were what you would call "clean" foods. All Natural produce, meat and vegetables.
Their exercise was minimum of 22 miles of running or walking a week, plus whatever else they did.
The Negative effects CONTINUED for a long time even after the Experiment was over.
I don`t think you read any of it.
Running and walking is not resistance exercise, why would your body hold on to muscle if you don't force it to.
Actually, excessive cardio vascular work combined with low calorie diet is not a good idea if you're trying to hold on to muscle.
Have you read the following study?
http://www.ncbi.nlm.nih.gov/pubmed/10204826 (this basically blows holes though your hexagram argumentative mindset)
The negative affects were physiological in nature, these dudes did not have the mindset and understanding of a bodybuilder, so it's understandable that they continued to gorge themselves after the study ended.
It's the classic fatso dieting mentality, doing something short term, then going back to eating buckets of ice cream and pizza pies.
You like to argue too much for no good reason.