The crystal was being used by humans who knew nothing of how it actually worked, so they time traveled by accident. The Precursors allowed themselves to be driven to extinction because they were curious what it was like. They were in no real danger though because they are transcendent, so they could just make new forms for themselves. The flood was created after 1000 precursors reduced themselves to dust to be revived at a later date. Then after round 10 million years these remains became corrupted, were consumed by animals and became the Flood. The guy who used the Flood in his plan to wipeout the Forerunners was the Primordial who was imprisoned by the Precursors who presumably didn't want him to kill the Forerunners, so it wasn't a last resort really.