Just reread Primordium and I realised what this meant. When Chakas and the Didact were questioning the Primordium, it revealed that the Flood was meant as a means to bring unity to all in the galaxy, at the cost of immense pain. The Flood will always be around, since there is no cure and no immunity. Forthencho sums this up, saying, "No immunity and no cure. There is only struggle, or succumb. Either way, the Primordial will have its due. We have met our creators, they have given us the answers we sought - and that is our curse." The humans were horrified by this truth - there was no way to eradicate the Flood, so their ultimate fate was either eternal struggle or eternal pain as a host to the Shaping Sickness.