But the idea is that without rational thinking skills, you have no way of knowing whether you're in a typical or atypical place to be obedient.
Imagine there was once an atypically good society that collapsed, and it turns out that all the people who brought it down happened to be freethinkers. Does that mean we should raise children to be obedient rather than freethinkers?
The important question is: are freethinkers brought up in our society more likely to go in the ‘right’ direction against the status quo? The example in the OP is only weak evidence for this, because its a lot easier to find moral actions ‘less evil than Nazis’ than ‘more evil than Nazis’.
A while back I did a couple of posts on the care and feeding of young rationalists. Though it is not new, I recently found a truly excellent post on this topic, in Dale Mcgowan's blog, The Meming of Life. The post details a survey carried out on ordinary citizens of Hitler's Germany, searching for correlations between style of upbringing, and adult moral decisions.