If you kill everything the Flood feed on now, and thus starve the Flood into extinction, then future species will evolve and thrive and need never fear the Flood. But if you let the Flood spread across the entire galaxy unchecked, and do nothing to stop it, it basically leaves all life doomed forever.
Also, the original plan the Forerunners had was to hide away while the Halos fired and then pop back out to repopulate the universe, and they were actually trying to archive various species in Shield Worlds and in The Ark, but shit went wrong (at least partly because they were betrayed by their own AI, and partly because they were having political disagreements right up to the very end), and things didn't quite work out the way they'd intended.
It's also worth remembering that the plot of the original games and the plot of the games now are technically different, because 343's version of the story is different from what Bungie originally intended. So the reasons for why certain things turned out the way they did is kind of different based on whether or not you're talking about 343's current version of the story, or the story Bungie had in mind when they were actually writing the original games.
SPOILERS
---
"I live my life 3 videogames at a time. Nothing else matters. Not the mortgage, not my clan and their BS. For those 3 games or less, I'm free."