I understand Nintendo's position and fear here. They receive damaging exposure(and threats of legal action) for things like this. It's very easy to downplay their worries, especially as a company that thrives on a reputation of being a 'kid-friendly' company.
However, I don't think this is the correct response. Once you set a precedent for accepting responsibility for these things, where does it end? When will adults and responsible users ever NOT be punished for the actions of (a few?) minors? Should users always expect limited communication services on Nintendo devices, due to the company's fears? When does it fall on the parents to take proper responsibility for their children?
That said, suspending the service could have been simply to allow Nintendo some time to make both software changes, and changes to the terms of service/user agreement that could better protect themselves, as a company, against any situation that could relate to the misuse of software like swapnote. I'd be very surprised if it's not back up by early January, the latest.