I've been following this, and I've decided it's time to chime in from across The Pond.

First:

I am searching my memory, but I can't think of any people who would treat children like that....

It is my experience that indoctrination of the youth is exactly how religions perpetuate themselves.  I don't think it's any coincidence that if you're born in Israel you will probably be Jewish, in Saudi Arabia a Muslim, in India a Hindu, in Italy a Catholic, etc.  Here in the US even a moderate denomination such as the ELCA (our equivalent of Germany's Evangelische Kirche) practices this, and the less tolerant Lutheran branches, such as the Missouri and Wisconsin Synods, run their own schools to keep their children from being tainted by public school educations.  The Catholic Church maintains a parochial school system that it established in the 1800s so Catholic children would not be subjected to the Protestant education that was the core of the public schools at the time.

Second:

I am not sure that discrimination by religious people is increasing or not....

It is.  Every year a significant bloc of Christians proclaim that the rest of us have declared a "War on Christmas," and then they declare war on us.  People who say "Happy Holidays" instead of "Merry Christmas" are assaulted.  Stores whose personnel say "Happy Holidays" are picketed and boycotted.  And now we have scores of legislative proposals (some of which have already passed) making it "legal" to practice discrimination in housing, accommodation, and services if your religious beliefs tell you to.  What these laws in fact say is, "Your right to practice your religion to the detriment of other citizens is more important than those citizens' rights to buy or rent a home, travel, receive medical care, marry, raise children, or anything else."  Anyone who doesn't see a problem with this isn't bothering to look.

Third, I read the New Statesman and New Republic articles.  I wholly agree with Chotiner, and I go on to say Odone is unequivocally full of crap.  I love how she magically morphs not being allowed to use public facilities to promote discrimination into the allegation that religious people "are no longer free to express any belief."  Such compelling logic.  The rest of that article is no better, and when she starts writing about people closing their businesses and losing their jobs, she truly lets her ignorance fly.  We don't let businesses discriminate because we've been down that road, and it isn't good.  Before the civil rights statutes, non-whites effectively could not travel in much of the US.  They couldn't get a room, or a meal, or medical attention, or much of anything else in the way of services and accommodations.  So we passed laws that say, "If you want to discriminate, you'd better get into a business other than serving the general public."  As for the registrar being fired, is Odone really that stupid (I do not equate ignorance and stupidity per se, but I do consider willful ignorance to be stupid.)?  A registrar is a public official.  Why should a public official remain in office will discriminating against citizens contrary to law?  What's next, the Grand Dragon of the KKK gets to be head of the Human Rights Commission even though he believes in discrimination against non-whites and non-Protestants?  Lunacy.

One more point on Odone.  She asks, "Can the decline in the social and intellectual standing of faith be checked, or even reversed?"  Let me give you a tip, Cristina.  People who want to be considered intellectually significant do not end discussions and debates, implicitly or explicitly, with, "You may not agree with me now, but you will when God condemns you to Hell for eternity."