Just a theory, but I'm fairly certain it is because the forerunners had no -blam!- clue what the flood was, where it came from, why it was unable to coexist peacefully, and if the flood they were fighting was the only flood in existance. so by keeping flood specimens for study after the halo array was fired, if another flood outbreak occured, they would perhaps have a way by then to defeat them without nuking all sentient life.