Why is Joseph's death necessary to think there may be a new era for Waknuk and the Fringe in Wyndham's The Chrysalids?
An era ends with the death of Joseph Strorm. Neither the Fringes, nor Waknuk will be the same again.
It seems a bit of a misnomer to suggest that it is Joseph's death that will produces a new era for the Fringes and Waknuk. If you believe the Sealand lady, all who were on the battlefield (including Gordon, Joseph's spider-like brother, and Sophie) died under the influence of the web-like stuff drifted down upon them by the Sealanders from their aircraft (which might resemble a Zeppelin since it is fish-shaped). A seemingly better conclusion might be that Joseph's death, Gordon's death, and the deaths of all who followed them--either physically or in heart or both ways--was necessary to start a new era. This is especially so since the Sealand lady says the Waknukian way of thinking and living had grown obsolete and would soon vanish altogether.
However, if you want to explore the isolated importance of Joseph and ignore the importance of his counter-part, Gordon, then we can identify one or two points that make his death necessary. First of all, his followers are entirely dependent upon the fear and tyranny of Joseph's leadership: not many have the fortitude to condemn innocents to the slaughter of a purge. Without Joseph's iron-grip leadership, the adamance for purging and crop-burning will without doubt wane. The zealousness for the cause will wane and the cause seem less significant.
Secondly, there are already others in the community like Uncle Axel and Uncle Angus Morton who reject the ways and beliefs embodied in Joseph's tyranny.
The moment [Joseph] set eyes on the huge creatures standing twenty-six hands ... [he] turned his back ... in disgust ... with a demand that they should be destroyed as Offenses.
They will surely step to the fore as new guides if not outright leaders. They will shape the new attitudes of the citizens of Waknuk, and their influence will spread wider than Waknuk. These two points affect the Fringes because if deviations are sought, feared, and punished with less zealousness, then there will be fewer sent to the Fringes. It is even conceivable that those in the Fringes might eventually venture into the civilization of Waknuk.
In addition, Rachael and Michael are left behind in Waknuk, at least temporarily. Their presence will surely over time alter the way deviants are perceived. They may even convert some to the acceptance of beneficial deviations and may encourage other secret telepaths to step forward. Or, when other telepaths are born, they will provide a safe and welcoming place for the new telepaths.
With these three factors combined, the silencing and incapacitation of Joseph's followers + like-minded folk with Axel and Angus + Rachael and Michael remaining (though with the aim of leaving for Sealand)--dependent as each of these are upon Joseph's death--the survival of the group and the beginning of a new era for Waknuk and the Fringes seems entirely possible.
[Michael]: "Now I want you to tell her this," Michael went on carefully. "She is to go on being brave--and very careful--and in a little time, three or four days, perhaps, I shall come and fetch her away. Will you tell her that? ... Besides, how could we stay now, knowing that there is a place for people like us, that there is somewhere to go?"