Very insightful question! Well, I guess it depends on who you ask. In the novel, the woman from Sealand definitely thinks that Waknuk deserves to die, and in fact, that it is inevitable. Consider how she explains her position:
"The Old People brought down Tribulation, and were broken intro 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..."
She continues in this vein, only ending her diatribe (which is rather sermon-like) with this somewhat concerning statement: "We have a new world to conquer: they have only a lost cause to lose." So, from her perspective, the Waknuk community and others like it represent one of the "fragments" or remnants of old humanity, which has shown itself so incapable of accepting the realities of the new world and the evolution of humanity. Because of this, and their desire to achieve the stasis of the human form is what sounds out their death knell.
Whilst the novel seems to make it clear that we are shown a species in the middle of a massive transition (as the chrysalids of the title implies), this does not stop her words from sounding harsh and brutal. This, in my mind, raises questions about the supposed humanity of the new kind of species, that is so willing to consign its fore bearers to the grave, and also gives rise to doubts about whether the new humans will actually do any better than the old ones.