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’.
This criticism would be valid if the study considered someone who neither opposed nor actively supported Nazi crimes as a 'rescuer'. But since the Uncommitted are filed as 'non-rescuers', the study does indeed single out the free-thinkers' tendency to go against the status quo.
Furthermore, the fact that the crimes of Nazism are considered among the most repugnant in history is only weakly relevant. As long as the society-encouraged activities are sufficiently offensive that in the lack of supporting propaganda they would be suffer universal condemnation, the more important trait is that the consequences for pursuing an unconventional morality were far harsher under the Nazi regime than in most other situations - and one had little personal gain to find there as well. This danger strongly ties anti-Nazi activity to a sense of personal moral duty.
If freethinking is a prerequisite for going against the status quo, and practically anything is better than the status quo, then don't be surprised when people behaving better than the status quo are all freethinkers. The fact that freethinkers went in the 'right' direction against the status quo is unremarkable* to the extent that the status quo was 'wrong'.
As for freethinking causing better morality: here is a freethinker who acted under a sense of personal moral duty, facing harsh consequences for little personal gain.
I'm not saying we shouldn't bring ...
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.