Should I only go for new copies, or is this soundtrack, because it was produced by Club Nintendo, relatively safe from bootlegging?
I don't know specifically what the situation is regarding the bootleg-to-authentic ratio in terms of Mario Galaxy OSTs, but you should know that no release is ever "safe" from bootlegging; if they can get their hands on it (and they can), it can be copied and distributed. Also, I'm not sure what you mean by buying only "new copies" and how that would protect you from getting a boot -- even the fakes come new and sealed in plastic, so that's not a reliable method.
That being said, the only auction up right now whose seller I recognize is this one:
http://cgi.ebay.com/Super-Mario-Galaxy- … dZViewItem
champ_des_pins is a trustworthy and respected seller, and many on this board (including myself) have dealt with him repeatedly over the years and have only good things to say about him. If you buy from him, you're guaranteed the genuine article.
Generally if the seller is located in Japan the item will probably be genuine, but I'm sure there are exceptions to this as well. There are only a handful of eBay sellers I will buy from when it comes to VGM or anime CDs, and I've gotten all their names from reading these boards and finding out who people trust.