The criticism that the participants were just doing as they were told has always seemed to me as rather missing the point. What better demonstration is there of the human capacity for cruelty than a bunch of Stanford undergrads torturing other students because a professor told them to?
What I find interesting are the people who are absolutely fanatical about disputing Zimbardo's conclusions. It's as if it's very important to them personally to be able to classify potential perpetrators of atrocities into two simplistic categories, People Who Do Stuff Like That and People Who, Somehow, Magically, Don't. Any experiments that might reveal human nature as the ultimate culprit are considered politically…
What you're misrepresenting as "fanaticism" is simply a strong but justified emotional reaction to what the debunking of Zimbardo implies.
An emotional reaction triggered by the revelation of a revealed hostile bias against normal people just like themselves by formerly trusted scientists, formerly trusted journalists, and other formerly trusted opinion leaders.
Interesting times ahead.