The flood would infect anything that would die giving halo universe an overwhelming force (pun intended) to deal with. And if that doesn't work forerunners could compose the Jedi. And if that doesn't work the covenant and forerunners could team up and surprise glass Star Wars planets. And if that doesn't work the unsc could strategically place havoc bombs. And if that doesn't work the forerunners could create an Ark far from the Halos and remote detonate them.