I think these two paragraphs constitute the essence of Andrew Lilico's argument that creationism should be permitted in science classes. If they don't, and I've distorted his argument by choosing them, then hopefully he will correct me:
1) "Otherwise, we are insisting that the children of millions of Christian, Islamic and Jewish parents be sent to school so that their parents' beliefs can be rubbished."
2) "We want children to attain some grasp of the nature of the world, to learn how to think according to the scientific method, to be animated by wonder about the world, to learn sufficient basics to inform their practical lives, to have enough grounding that they can go on to further study if they so choose."
The first argument really only works as a caution against going too far. There is no need for science teaching to adopt a confrontational attitude to religion and make claims to a broad rebuttal of anyone's religious faith. Topics like evolution can be taught while leaving any philosophical implications to be worked out by the student outside the classroom as part of their own process of moral development. That is better than trying to make sure everyone is equally offended. Including a range of alternatives to evolution in the classroom will result in more children being taught things that their parents don't believe, after all.
I think that Andrew's second argument broadens the function of science teaching too far. It is telling that he extends his argument from creationism to "the political implications of global warming, the ethics of abortion, the social issues around MMR scares, or (I submit) issues in philosophy of science (such as instrumentalist accounts of scientific models - cf Bishop Berkeley - or the merits or otherwise of Intelligent Design theories in the development of biological engineering) or indeed questions relating to the origins of the physical universe (creationism/accident/no-beginning universe) and even to the origins of humankind (Darwinian evolution, Lamarckian theories, game theoretic accounts, Young Earth Creationism - some of these having strong empirical support, others virtual empirical refutation, and that is of course something that should be pointed out)."
There are two problems with this. First, it is hard to believe that schools are really equipped to teach subjects as subjective and contentious as the ethics of abortion or the political implications of global warming. This problem will be felt in any unscientific debate brought into a science class. There isn't any way to form a meaningful curriculum and it will be a rare teacher who can address these subjects without their personal opinions creeping in. Again, that is something that children should work out for themselves outside the classroom where there will be just as much bias around but hopefully, at least, a plurality of opinions.
We also need to consider why we give such attention to science, making it a compulsory subject that gets such attention in the classroom. The answer, surely, is that the scientific method has proved uniquely productive in providing a range of public goods and enabling ordinary people to think their way around important problems. For that reason we have a unique interest in promoting an interest in science. That way we can get more scientists and try to make sure enough of the rest of us are interested as well. If you start bringing in a series of issues that are essentially philosophical or political in nature you contaminate classes that should be restricted to study within the scientific method. In that way, you weaken children's understanding of what science is and how they can approach concrete questions using its principles.
Creationism has never functioned within the bounds of the scientific method and it would therefore undermine the effectiveness of science teaching.