This question was categorized in The Chrysalids section of Enotes, so I am going to assume that the society being referenced is Waknuk society.
No, I do not think that John Wyndam likes the Waknuk society. It's hard to tell if he has problems with their staunch religious biasing, or if he has problems with the massive amounts of discrimination that the society encourages. Maybe both. It doesn't really matter, because I feel that it is clear that Wyndam doesn't like Waknuk society.
My main reason for why I think that Wyndam is anti-Waknuk is because he made the entire society the antagonist of the story. When an author makes somebody or something the bad guy, that's usually a fairly clear indicator of the author not liking it or the characteristics of it. Already beginning at chapter 1, the reader is clued into the fact that Waknuk society is bigoted and close minded. That's why Sophie must hide her extra toe from everybody. As the reader grows closer to David, the reader begins to like David more and more. And since David is starting to dislike Waknuk society, so does the reader. If Wyndam actually liked Waknuk society, I don't believe he could have made the reader hate the Waknuk's so effectively.