Clash of Cultures in Australia

The Sydney Morning Herald contains an article on the potential of class warfare because of the controversy regarding "faith-based" schools. The article is in the form of a point-counterpoint between detractors of faith-based schools and their supporters, represented by John Kay of the Greens Party and Stephen O'Doherty, of Christian Schools Australia. Kay begins:

Alarm bells start sounding when young people leave school confused about the boundaries between faith and evidence. They get even louder when the penny drops on the massive state and federal funding that supports the growth of schools that systematically mislead their students. And they reach a crescendo when governments are caught accepting the distortion of education in faith-based private schools.

Mr. O'Doherty responds:

Is it just me or has anyone else noticed that the arguments against choice in schooling are becoming increasingly divisive and anti-religious? With the school funding issue taken off the table by the Federal Government, at least for the time being, the anti-choice debate has taken on a much nastier tone. The old cliches are creeping back in. People with religious faith are increasingly targeted as narrow minded or anti-intellectual. Too often arguments against faith-based schooling adopt the patronising tone of superior knowledge.

Once again, I wonder what the correct position on this is. My son Marcus just got back his second grade Stanford Achievement Test scores and one thing leaped off the page at me. When compared to other students nationwide—presumably national public school children, he did better than between 70 and 98 percent of them, depending on the subject. When compared to other Christian school students (I haven't tracked down what that sample is yet), however, he was largely just above average. In several scores, he was below average for the grade. What accounts for this, I wonder. Are the kids in faith-based schools getting that much better of an education than the public schools? The perception among Christian parents certainly is that. It seems that, albeit with a sample size of one, it is borne out here. Wouldn't you want to put your children in a school that gave them the best education?
When does the problem with science rear its ugly head? I know I am going to have to write Marcus' curriculum when it gets to the natural sciences because most of the established curricula veer off the rails when it comes to evolution. Thoughts?