"This installation was specifically built to study and contain the Flood. Their survival as a race was dependent upon it. I am grateful to see that some of them survived to reproduce."
Now, the way I understand that the Flood works is that they infect a host with spores, which take over the body and slowly convert some of the body's cells to Flood spores and eventually Rangers in the Carrier form. This sounds like how a virus works, by exchanging the cells' DNA for the virus DNA. If that's true, then as the Flood spreads, the "pure" Flood DNA that started out will change relative to the hosts they are taking, and so once the Flood spreads the DNA will no longer be pure. Now, if you assume that in the above quote the Monitor is talking about the Flood's survival (a point of debate in itself), then you could go along to say that the Forerunner want the Flood to stay genetically "pure", for some reason.
But why would they want this? My first thought was that maybe the Forerunner were intergalactic racists or something. After a bit of thought I've come up with a better idea. Some time ago I was reading about organic computers - that is, computers made of living tissue. These computers can process information faster, and also store a lot more information, than silicon-based computers. However, silicon is a lot more sturdy than most organic tissue, so it doesn't really make sense. However, suppose you used DNA to store information - it already stores genetic information, after all - you would genetic memory in the most literal sense. If you used DNA to store information, you would have to make sure the organisms would survive, for one, and not mutate or change DNA, for another. That means engineering some incredibly sturdy and long-living organisms that reproduce asexually (without a partner; i.e., by cloning themselves) - an almost perfect description of Flood spores. Now, obviously you'd want to enact measures to make sure these organisms don't spread and also make sure you'd be able to study them, stopping the small amount of mutations that would occur. Of course, there's the question of what information could be so important to warrant wiping out all life in the galaxy in order to preserve it? Well, perhaps Forerunner genetic information, secrets of the universe, or even the ultimate question to the ultimate answer of life, the universe, and everything. (heh)
...Given that the human brain can whip the best computers in the world up and down in some processing disciplines, a being that is 10 feet in diameter, and probably 60% - 80% brain matter would make a very formidable computing engine.