Sometimes I think everyone should be required to wear a sign stapled to their foreheads outlining their religious (or non) beliefs and their policies on greetings and gift giving. I think it's gotten quite out of hand and is very confusing.
From an etiquette perspective, I cannot see where you went wrong, OP. Your daughter gave a small gift to her classmates as a kind gesture. You even went to extra lengths to ensure that it was neutral and would offend no one. Yet, it did, either because it was perceived as still too religious in nature, or because it wasn't religious enough.
We read often on this board about what to do in the event someone receives a gift that they do not like, can't use, find offensive, etc. Isn't the etiquette of the situation that one should graciously accept the gift with thanks in the spirit in which it was given, and then privately use or dispose of the item as one likes? So, from that standpoint, the parents of the child who received your daughter's kind gift not only alienated the parents of their child's classmate, but expressed their opinions (however valid or not) about her gift in the most nasty, rude and ill-mannered way possible, short of leaving a flaming bag of...something...on your front stoop.
All I can say is wow. What a way to teach your kid to be ungrateful and rude. I feel sorry for the little kid.
I really think etiquette should be required curriculum in school, like reading, writing and arithmetic.
OP, I think you did nothing wrong. And your daughter sounds like she is growing into a fine young lady with a kind heart. If there was a mistake made by you in giving the gift, it was the mistake of a generous heart.
And if the recipient's parents are offended (which I don't personally think they should be, but have the right nonetheless) the way they followed up was, in my opinion, a horrible breach of etiquette. I'm so sorry this happened to you.