My 14 year-old son fancies himself a deep thinker/seeker, and our spiritual "household culture" conforms to your "unexamined faith" mantra: we try to encourage independent examination and free discussion. This has recently led to a roadblock that's got me stumped, and I'm hoping you might share some wisdom. My son is a Boy Scout. He loves scouting and wants to go "all the way." But last night he was sent home from the troop meeting for refusing to stand for the Pledge, explaining -- quite respectfully -- that the "justice for all" line has come to be a violation of his conscience. Though shocked, my reaction was "first, do no harm." I told him I appreciated his conviction and admired his courage in risking his standing in the eyes of adult leaders whom he greatly admires, as well as boys he likes and respects. I know that "a man convinced against his will is of the same opinion still," and thus do not want to browbeat him into submission. You know how much he's invested to this point and how much he'll be throwing away if he chooses to "die" on this hill. Tormented is too severe, but deeply vexed is close to the mark. As a reasonable man and an Eagle Scout, I am hoping you will offer some insight.
You have expressed the issue eloquently, with words I would have been proud to pen. And surely your son is right (and wise beyond his years). Justice for all is something we would like to believe is reality, yet no one watching the nightly news is likely to be deceived.
As for the dilemma, I would suggest that a way forward is to stand, but not say the offending words. Just like at church when we're singing a song verse that I cannot in good conscience sing (e.g. "We are often destitute..." -- since I'm not!), I simply close my mouth, or perhaps hum. That is, there's not need for him to call attention to himself. He could stand and not speak, or stand and utter only the words he believes in. If he believes in pledging at all...
The deeper question might perhaps be whether we can totally pledge complete allegiance to any authority other than Jesus. If "allegiance" means only we want to be good citizens (something commanded in the Bible anyway), then there may be no problem. But if we are guaranteeing -- giving out word -- that no matter what we will obey the government, then that's another matter entirely. Consider the book of Daniel. Daniel (chapter 6) and his three friends (chapter 3) wouldn't budge if it meant relaxing their allegiance to the Lord. They knew that nothing can rightfully usurp God's position of paramountcy.
Finally, I suspect that though in the majority, your son is in very good company. I was not brought up in a household of faith, and so during my 5 years with the Scouts I never resisted saying what they told me to say. Is this counsel of any help?