I can't judge, and without knowing more about your relationship and the particulars of the interaction...I don't think anyone can. Me personally...I would have sent back a generic "Happy Holidays" - or "Go Festivus Yourself" message, instead of trying to make it a theological issue. That is only b/c I know it is a very unique situation where you can talk about your lack of believe in religion and be effective. Most don't want to hear it, just as you wouldn't want get a video telling you why Jesus is what Christmas (and your life in general) is all about. My 2 cents...

EDIT - the fact that you are on here asking complete strangers to pass judgement on a situation we are ignorant about, I will guess you feel it was wrong, at least a little - and that is the important thing, esp. if you feel you wronged a friend.

I'm going to take a leap here not everyone will be able, or willing, to take with me and say that it was wrong. Basing my opinion on the following assumptions:1. You called this person a friend not acquaintance, which to me infers some sort of relationship outside of christian witnessing. 2. Being a friend, I also infer some level of respect. If I'm wrong on those two counts, please disregard what follows.
Otherwise, I find the response to be disrespectful. Not all Christians or believers are dumb arses, and not all atheist are arse holes, and I chose not to perpetuate that generalization. Your friends intention was likely a benevolent one (as you called it a greeting, not an invitation to be saved), and you basically gave them the finger. My mother is uber religions and though she has ceased trying to bring me to jesus and most of our conversation is sans religion, I still have to swallow a lot of religious undertones. When she talks about praying for people, what I hear is that she's sending good wishes to the stars for them. Awesome. Who in this world can't use a little positive mojo thrown their way? Many believers seem to find it difficult to not include religious undertones in their communication and while it may be annoying as f#$k, you are still responsible for your own intentions and should consider that when choosing your response. I admittedly used to be much more snap judgement and in your face with my responses to such greetings, but find a much more sustainable peace and fulfillment in my own life when taking greater responsibility for my own intentions before responding.

Depends on your friend, really. If they embrace you and your atheism, then I am sure it is fine. If they do not, or if they view you as a project for "saving" or some other form of conversion, then their response may be different.