Here's the breakdown as I see it:

Adults in charge lead prayer - No.  This is religious indoctrination.

Adults in charge provide a set opportunity and children "spontaneously" lead prayer - No.  This is just religious indoctrination by proxy.  The adults are still controlling the situation to generate their desired outcome.

Some kid happens to ask to lead a prayer, even if this becomes a regular occurence - Yes.  My instructions to our kids would be to respectfully bow their heads and wait for the prayer to finish.  This is an overwhelmingly religious country and they need to get used to people praying in all kinds of venues and expecting them to at least bow their heads and wait.  The cost to them is small and it is important to others. 

My larger fear:  As I said, we're not trying to teach our children to be atheists, but rather free thinkers.  For instance, the oldest just turned four and the topic of God, or rather no God, has not come up once in those four years.  (Contrast that with a Christian household.)  We have never told him what we believe on this topic.  He wouldn't understand it anyway, so all we could do is indoctrinate (which we're perfectly willing to do on lots of things).  But there will come a day when those questions do start and I intend to be very matter of fact.  I won't say, "We Voljeans are..." or "This family believes....", but I will explain as best I can given the comprehension capabilities he has at the time.

I hope that day is as far into the future as possible.

Despite this approach it is still likely that our children will mimic our lack of faith.  They will not have had their neural pathways shaped by a thousand chants of, "Jesus loves me this I know.  For the Bible tells me so."  And of course we're their parents. 

So when that day comes our children (likely the younger one at the same time because all information is shared when you're only 18 months apart) will probably believe something that is patently offensive to most Americans.

You may not remember this, but many years ago on this board you and I had an exchange on that very topic.  The thread was on the origin of the universe and someone asked, "So where did God come from?"  When I replied, "Our imagination." you asked me if I realized how offensive that statement was.  

And it is.  But, as was explained in the thread, it is not a statement crafted to offend like comparing the other political party to Nazis or saying only an idiot believes something, but rather a matter of fact statement of position.  The biologist Richard Dawkins has a reputation for expressing atheism in ways that just inflame believers even more.  If you look at his YouTube clips however, for the most part he really is not trying to inflame.  Yes, it does piss people off, but he really is just explaining the positions.  And to believers those positions are offensive in ways that other faiths are not.  The problem is not the medium, but the message.  Does someone believe he is communicating with God when he prays?  Dawkins explains to the man that he has a delusion.  He's not calling the guy a poo-poo head.  He is simply explaining the man's experience as he (and any atheist) sees it. 

And it is very offensive to most Christians.  From what I have seen, it offends far more than differences of opinion on any other topic, including differences between faiths (just look a survey data on what would be unacceptable for a president to believe).  This is why atheists have for the most part learned to keep their darn mouths shut.

I give people like you and InspectorVol for whom faith is obviously a very important part of your lives a lot of credit for sticking around a venue where several heathens are comfortable spouting off.  But it is worth noting that you have been well desensitized.  You welcome hearing what we say, but make no mistake, you are not normal.  (Sorry about that. 

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So my biggest fear regarding faith and my children is not other people praying or talking about their faith and telling their stories, but  what will happen when as children (if my prediction is correct) the little Voljeans contradict what the other adults and children believe.  Note that 57% of Americans don't even believe a person can be moral without a belief in God and likely teach that prejudice to their children.  This could get ugly in so many ways.  They could face ostracism, made to feel ashamed or even see expressing atheism as a way to shock and generate attention (albiet negative attention).  I want that day as far into the future as possible.

As a parent of young kids who have not yet crossed this bridge I would be interested in hearing of the experiences of others.