Sadly, this is often the equivalent of tilting at windmills. The kids' blind conformity and fanatical adherence to their peer group norms, and their fervor to ruthlessly punish and ostracize their peers who fail to live up to them or who end up assigned low status according to them, is rarely matched by even the most fanatical and close-minded adults.
As Bongo said, "teach them to hide it". That is, let them know that they can outwardly go along with peer group standards while inwardly reserving judgment, or holding a different judgment. Also, teaching kids social skills (primarily, how to make friends) allows them to participate in multiple, sometimes overlapping groups. That will enhance the ability to reserve judgment, first on what the groups differ on, and later also on what they share.
Part of the point of teaching independence of thought is so that it can lead to independent action, so there's got to be more than going along while thinking your own thoughts.
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.