Great question! I think it is important to focus on the setting of the story as well as the title to think through this question. Remember, in America, this story was first published as The Re-Birth. This is somewhat less subtle than Wyndham's initial choice of The Chrysalids, but both capture the sense of humanity evolving and becoming something different and new after the Tribulation - the nuclear disaster that has destroyed the world as we know it. In particular, the title The Chrysalids for me symbolises humanity in a state of transition - it is neither caterpillar any more (in spite of the efforts of those in Waknuk) yet it has not yet become the beautiful butterfly that is ready to break free from its chrysalis and fly away. Thus David and his friends are forced to keep silent about the truth because they know that if they are discovered they will be at best sterilised and exiled to the Fringes, and at worst killed.
However, the voice who talks about this stage of transition most clearly is the woman from Sealand, who in Chapter 14 says:
"Neither his kind, nor his kind of thinking will survive long. They are the crown of creation, they are ambition fulfilled - they have nowhere more to go. But life is change, that is how it differs from the rocks, change is its very nature...
The Old People brought down Tribulation, and were broken into fragments by it. Your father and his kind are a part of those fragments. They have become history without being aware of it. They are determined still that there is a final form to defend: soon they will attain the stability they strive for, in the only form it is granted - a place among the fossils..."
According to her, therefore, the future of humanity is clear. It does not lie with the Waknuk community and its desperate attempts to hold back evolution, but with the people of Sealand.