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 up freethinkers - just that in isolation, this study doesn't make make the decision a slam dunk, despite the superficially impressive "21 times" figure.
*EDIT- Potential ambiguity: By unremarkable I mean the evidence provided by the study shouldn't have much of an effect on your prior of 'freethinking makes better citizens'. I don't mean it as "of course you'd expect freethinkers to be better citizens!".
Ah, I misunderstood you: I thought you were suggesting the possibility that free-thinkers wouldn't be motivated to rebel at all without a sufficiently offensive status quo, not that they might do it in an unexpected direction.
Regarding Kaczynski, while he's certainly an example of society-unfriendly morality, I suspect we would still be a lot better off if everyone had the willpower to go that far, if necessary, in pursue of their concept of greater good. In other words, the damage Kaczynski did arose from the combination of zealous nonconformism and a dee...
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.