Stability and stagnation are two very different things. When one is stable, he is comfortable and lives with less worries because of the predictability granted with stability. Stagnation comes when the individual (or individuals) are no longer allowed to grow and to expand their horizons. When we are no longer able to learn and when we no longer have the potential for change comes stagnation.
In The Chrysalids, the community is not permitted to grow and change as individuals. Because they aren't able to think for themselves, and because they don't allow differences, any opportunity to develop as individuals or as a community has been stripped away. This is why we say that the community is in a state of stagnation. In addition, the word chrysalis itself means an enclosure or a tight cocoon where a butterfly in the pupa stage is enclosed. This is a very similar definition to the community created by the author.