First, there is no way you were rude. Your sister asked an honest question and got an honest answer. (Non)problem solved.
Second, forum bully is crazy. Some people just hate atheism and will jump on any chance to be offended by something an atheist does. If you had accepted the nativity scene, she would have been offended because your heathen child wouldn't have the proper religious reverence while playing with it or something.
Third, Christmas as it is currently celebrated by the majority of the US population is primarily about Santa Claus, Christmas trees, gift-giving, and other non-religious cultural traditions. The actual birth of Jesus is not exactly at the forefront, at least in our popular culture. (I understand it's unlikely Jesus was even born during the winter and Dec. 25 was mainly chosen to integrate pagan winter solstice celebrations.) I find it rude to say that non-Christians shouldn't celebrate the non-religious/non-Christian aspects of the holiday.
Finally, I'll add my own thoughts as an atheist parent. I'm pretty laid back because I was raised with religion (Jewish with some exposure to Catholicism on my dad's side) and have still been able to form my own beliefs. If DD's grandparents want to take her to Church/Temple, read her Bible stories, etc., I won't object if she doesn't (barring actual pressure to believe or convert). My feeling is that being exposed to different beliefs and cultures can only be a good thing. Personally, I wouldn't mind a Noah's Ark theme; it's a good story, and I'm a supporter of reading the Bible as literature because it's so ingrained in our cultural consciousness and Biblical allusions are ubiquitous in literature. I would be uncomfortable with a nativity set, however, and I'm not sure I can really pinpoint the difference.