Paul's struggle throughout Dune is the race conciousness of all humanity gearing up towards war because of the stagnation of the genepool which has lasted since the monopoly of the Guild was made. He wants to stop the Jihad but knows that it had to happen to ensure humanity's survival in the long run..he just didn't push it far enough like his son & that's where he failed. Destroying the spice would stop the jihad..which is great but humanity will still continue to stagnate.

Paul's struggle throughout Dune is that the race conciousness of all humanity is gearing up towards war, because of the stagnation of the gene pool which has lasted since the monopoly of the Guild was made. He wants to stop the Jihad but knows that it had to happen to ensure humanity's survival in the long run; he just didn't push it far enough like his son, and that's where he failed. Destroying the spice would stop the jihad, which is great, but humanity will still continue to stagnate.