ONI has tried studying the Flood before, and it always ends in disaster. The Forerunners spent thousands of years trying to figure out a cure or to study them and it is simply impossible. The Flood itself is the undead remnants of the creator Gods of the Halo universe, it's simply impossible to contain and cure. Indeed it breaks several laws of physics itself. You're method of isolating a single cell like a modern cancer cell? that would doom the host, and likely whatever ecosystem he was living in. You just can't stop it.