I thought schools were supposed to make people think and engage in lively discussion? The topic of religion is not so "hot button" that it cannot even be brought up. If that is the case how can topics like the crusades be taught in history? What about more recent wars between islamic militant groups? Why is it that god can be mentioned in the pledge of allegiance (which is still recited daily in my son's school), but one child cannot ask another a question about whether they believe in god or not?
Maybe we just went to different schools, but I wasn't learning about the Crusades when I was 9. I understand that asking a fellow classmate about God is completely benign in and of itself, but there was a follow-up with a different classmate who couldn't believe someone didn't believe in God; that could very quickly spiral into bullying the outsider. I experienced a small amount of that myself when the other kids found out I didn't have a dad (although I didn't complain to my parents about it, because honestly, what the hell; you've got to learn to interact with your peers at some point). If there's a chance that something could be perceived as bullying, especially in our current state of heightened sensitivity about such things, the teacher has an obligation to nip it in the bud.
My parents were schoolteachers, so I got to see firsthand the level of bullshit that parents will throw at teachers if they're at all concerned that their kids might get bullied, and the teachers have to take that into account. I don't think anything the OP's daughter did qualifies as harassment, but as soon as a complaint has been made, the teacher has an obligation to let the parents know that an inappropriate topic was being discussed and caution the daughter against doing it again. And, let's be honest, if a complaint was made, it's very possible that the innocuous question already resulted in some bullying that made the child feel uncomfortable.
As for nipping something in the bud because of what it "might" lead to. Give me a break. She asked a legitimate question. The other person could have simply replied that she did not want to talk about her religious beliefs and the whole thing would be a non-issue. But no, lets insulate our kids from any remotely challenging thing they might face in the real world, because god . . . (I mean, "deity") forbid little johnny should think, much less feel bad, about anything.
They're 9-year-olds, not adults. You can't expect a child to respond with "I feel that's an inappropriately personal line of questioning and I choose not to answer." That would probably lead to more bullying than just saying "No, I don't believe in God." There's a time and place for those discussions to happen, but it's not on the playground, unsupervised, by fourth graders.
Another question - why is the fact that the question was asked on school grounds important? Per your rationale the school has an obligation to nip conversations like that in the bud, because of what they might lead to. Well, what if the question was asked 1 foot outside of school grounds? How would the school's actions be effective to address the hypothetical issues you are concerned about?
The school has a legal obligation when it comes to children in their care. If the child is considered to be in the school's care, even if it's off school grounds (say on a field trip), they still have a legal obligation to protect the children. I used to work for an elementary school (in a removed capacity), and they made us learn the laws about when a child is considered to be in care of the school. I've conveniently forgotten the actual statutes (I never actually worked with the kids, so they didn't really apply), but the basic gist of it was "you're responsible for the kid until the second you hand them over to a parent/guardian, regardless of if they leave school grounds." So, yes, there's a legitimate legal obligation on teachers/school staff to protect their students. And if a parent is filing a complaint saying the school failed in that duty, they have to take it seriously.
Finally - how does asking a single question constitute harassment? The charge is either ridiculous or OP is leaving out some major details.
From:
http://legal-dictionary.thefreedictionary.com/harassment
"harassment (either harris-meant or huh-rass-meant) n. the act of systematic and/or continued unwanted and annoying actions of one party or a group, including threats and demands. The purposes may vary, including racial prejudice, personal malice, an attempt to force someone to quit a job or grant sexual favors, apply illegal pressure to collect a bill, or merely gain sadistic pleasure from making someone fearful or anxious. Such activities may be the basis for a lawsuit if due to discrimination based on race or sex, a violation on the statutory limitations on collection agencies, involve revenge by an ex-spouse, or be shown to be a form of blackmail ("I'll stop bothering you, if you'll go to bed with me"). The victim may file a petition for a "stay away" (restraining) order, intended to prevent contact by the offensive party. A systematic pattern of harassment by an employee against another worker may subject the employer to a lawsuit for failure to protect the worker. (See: harass, sexual harassment)"
I never said what the daughter did was harassment, because I don't believe it was. It was an inappropriate topic to bring up, and I would assume it's being treated very leniently with a "let's not talk about that here" sort of attitude. If it's being treated as harassment, that's stupid. But part of learning how to interact with other people is when certain topics are considered unacceptable. If you're dealing with classmates or colleagues, best not to bring up religion or politics.