What is your relationship with this user? Have you spoken privately with them yet?
Since you have indicated that they are otherwise a valuable and helpful member of the community, your best course of action may be private, one-on-one communication.
- Addressing this users concerns will help to get them to settle down. Even if you can't take any action to resolve the concerns, you will have at least personally addressed and given attention to the user's complaints. If you've found something that you can action... great! You've gotten valuable feedback that improved your site.
- Attempt to create a dialog by sharing your opinions, and empathizing with the user's concerns where possible. If you disagree with the user, do so in a way that is persuasive and respectful.
- Acknowledgement of concerns will go much further in helping them integrate to the new site than disciplining the user for very understandably being reluctant to go along with a major change from the status quo.
I would like to reiterate that you don't want to discipline the user in this case, unless they are being exceptionally hostile. In my experience, these users have some emotional investment in the 'status quo' and acting in a way that would be perceived as hostile will likewise make them more hostile -- not only to you, but to the situation and the community. It is much better to reach out to them and to continue to make them feel welcome in your community.