My girlfriend attended catholic high school, and is still at sixth form there (sixth form is officially completely church free, but isn't really as it's all the same staff and building). She's not Catholic as, I believe, every religious school has to let a few students of different faiths in. The way she was spoken to/treat by the Catholic teachers was atrocious, she was heckled in RE for openly admitting being an atheist, was glared at by students and staff alike when she had to approach the front at the termly mass with a hand across her shoulder to show she wasn't baptised(or something like that). Every science lesson also ended with "scientists say this but we know if they are right, God made it happen" The way they treat kids in general isn't good either, results driven with no regard for a childs happiness. The motto of a catholic school on The Simpsons comes to mind; "Jesus suffered for our sins, now it's your turn".
All in all, I don't agree with religion in the classroom as it usually attempts to blur or blatantly disregard the truth. I haven't read the whole thread but I did read a few of the linked articles on the first page. speaking as a college student studying physics and chemistry, that one by the head of a science department is genuinely scary. Did he buy his degree online?