Could be that the Pequod government knew just fine that dissent isn't very closely tied to genetics, but wanted to make an example of what happens to dissenters pour encourager les autres. People thinking of dissenting have been put on notice that if they make waves, not only themselves but anyone they are even remotely related to will die; and those who don't buy the government line that the punished were genetically tainted are made aware that the government is perfectly capable of wiping out millions essentially at random just to make a point.