It is certainly appropriate. Although the most likely consequences is nothing much happens, whether you consider it risk free should depend upon how you view working for someone that gets upset upon receiving an expression of positive thought*.
Personally, while I would consider it unfortunate in the short term, I would consider it a long term benefit to know that a future supervisior is unable to control an irrational response. Given that ignoring this part of the email is an acceptably response, I would rather not work for someone that would respond negatively. If your religion inspires you to give goodwill to others in the name of your deity, then go for it.
*This is not to say that everyone should embrace Christmas, I understand that returning the same may actually be forbidden by ones religion, but that doesn't mean it can't be taken with good will, with any response being within the permitted bounds of the religion.
Edit: in response to the "risky" comment. That is exactly my point, if a supervisor focuses on the "who" instead of the "what" in "His Evilnesses blessing for the new year", I don't want to work for him. Totally ignore the comment, fine, smile and say thanks, fine, gets offended because my religion doesn't match up with his, and then feels an irrepressible need to share his displeasure, pass.