When I lived in Hingham, MA, a local Catholic school had issues with the child of gay parents and also with the child of divorced and remarried heterosexual parents. The issue made sense.
In both instances, the Catholic school contacted the parents and made it clear that their children would learn in school that homosexuality was a sin (as well as divorced parents living together, whose first marriage had not been annulled.
The school did say the children could attend but was concerned about undermining how their children viewed their parents. They also felt the two couples' children could be uncomfortable if other children thought that the children's parents were living "in sin".
If the parents were okay with that, the children could continue to attend the Catholic school. So, it was concern for the child, that drove the school to confirm with the parents that they were okay about what would happen.
You might not agree with what Catholics believe or in this instance Baptists, but most religions are not "a al carte" religions. One of the reasons, parents shell out the money they do for children to attend private religious schools is to reinforce their own religious beliefs and so it does present a challenge for schools when confronted with the situation of a "Zoey", how do they preach their beliefs without making a "Zoey" feel uncomfortable. Some of these schools think its unhealthy for the child to be in this environment and therefore unacceptable and others let the parents decide. But you seem incapable of seeing the issue from all sides.
In a sense, you are the bigoted one, since you refuse to accept anyone's beliefs that don't align with yours. Many religions preach homosexuality is a sin, but calling someone a sinner, does not mean you can't love them.
Jesus died because we are all sinners. His death was the ultimate "love sacrifice". But his death was for the forgiveness of sins and not to redefine sin.
As a Christian, I believe homosexuality is a sin. But then I am a sinner to, I just happen to have different vices. In that, sense I can connect with everyone, since we are all in the same boat.
If you can accept me as a sinner, I can accept you as a sinner. We are all sinners. But I won't pretend sin is not sin, whether it is your sin or mine.
I have hired gay people to senior executive positions at my company, their partners have been welcome at company functions, and we provided gay couples the same benefits as others. I support gay marriage (though I would prefer all legal marriages be contractual civil unions and marriage be reserved as a religious ceremony (I just had an acquaintance do that). A beautiful wedding, but no legal marriage, since they don't want California's community property laws to apply to their relationship. The woman did not trust the man's terrible spending habits.
But getting back to the point, religious schools exist precisely because they teach religious values, that others may agree or disagree with. It is precisely the difference in values between religious schools and public schools, that so many people of different religions or ethnicities choose to send their children to religious schools (Muslims frequently choose Catholic schools over public schools for their children (are you "anti-Muslim" too).
Bottomline, if the Baptist school went out of their way to hurt Zoey, that is wrong. But if the school simply recognized the problems that would arise especially for Zoey hearing on a regular basis that her parents were living in sin and were concerned for her and her family, then if fact, it could very well be the right thing for her not to go.
I tend to side with the Catholic church decision in my old town (I am not Catholic), that the school should let the parents decide, but they should be well aware of the values that will be taught and acknowledge them in writing and the potential cognitive dissonance that could cause Zoey.