Yes, the school should reject that child. I went to public schools for 1-5 grade, and a religious school for 6-8, and then back to public schools for high school. Religious teachings and a religious family atmosphere are a big part of many religious schools. The whole idea is not just to teach them how to read and write (though religious schools often do this far better than government schools), but to also put them in an environment that affirms and strengthens their faith and the faith of the family they were raised in. The school I went to in particular was fairly small, maybe 400 kids in grades 1-8 (though I only went 6-8). It was pretty special too. It was a joint collaboration between a local Catholic church and a local Protestant church (part of the Vineyard). Many of the families of the churches sent their kids to this school, coached teams, tutored students, etc. There were many get togethers between the churches where one would see schoolmates from the other church and so forth. I even went to a summer camp and later was a counselor at that same camp that was run through this school.
Now this is all important because it highlights how much family life, formal education, and religious studies are all tied together in many religious schools. A child with two homosexual guardians would be receiving drastically conflicting ideals from home and from school. It is unlikely the homosexual couple would participate in either participate in the church the school operates though, or share many of the same beliefs that most religious school teachers and clergy, and parents share. The conflict would go both ways. Not only would it be very confusing for the single child to have such contrasting views from different areas of their life, but other school children would also be subjected to those issues, perhaps before their parents are willing to tell them about those things.
One of the big reasons people send their children to religious schools is because they strongly disagree with the type of cultural atmosphere most public school have. If a parent does not want their child to be taught at school that homosexuality is OK, that is their right. And they have the right to send their child to a school that affirms these beliefs. Many modern religious schools exist with separating children from what many religious parents see as cultural rot, as one of their primary goals. Forcing a school to admit students whose guardians play a large role in that very same cultural rot would undermine one of the purposes of religious school, and the choices and beliefs of the other parents.
Edit: After reading the article, I am inclined to think that the two homosexuals in questions chose this school not as a realistic school choice, but with the primary purpose of either intimidating the school to backtrack on their beliefs, or to just make a general media spectacle of Christian schools. I think that they were motivated by radical politics far more than actual concern for the education of the child.
