i can't explain why they didn't Kill Sephiroth before they left the crator, that's a question for the game creators (could have just been a plot device to keep the story moving)... but, it looked to me like they took off like an explosion, like they were launched out of their place of slumber... think of it like a volcano going off, the lava doesn't flow back into the volcano during it's eruption rather it flows out in a violent explosion... after waking up they prolly didn't just go straight to cleansing the planet, they may have been groggy and took a few hours before starting their rampage, they have been sleeping for a long time after all, technicaly they were just born, since they were stopped before their chance to be born after they were first created...

even when i first played it i never got the impression they were designed to destroy everything, but rather i got from Bugenhagen & Ilfana's speaches was that they were designed to clean out all impurities like they were the equivelant of white blood cells... considering most humans were native to the planet they had no reason to destroy those that were not harming Gaia, but would take out the ones responsible for syphoning out the lifestream for their own ends, and those infected with JENOVA cells since JENOVA was not native to Gaia...