Simon: The main difference seems to be that people are motivated to do what they believe to be right. They don't necessarily do evil solely because of deference to authority.
I didn't get that from the Independent article. My take is that most people will supress their own conscience due to the influence of authority, not because they're evil, but because they want to please whoever is authority.
The article didn't dispute the facts about the Milgram experiment, just what motivated the majority of people to keep administering (what they believed to be) painful, even lethal, electric shocks.
Simon: It shows the importance of challenging and debunking bad ideas including the ones people follow because of religion.
It's important to keep in mind that, in academe, no one establishes a reptuation by agreeing with the status quo.