: Keeping the Flood in stasis was a gamble, but the Halos can not only nuke
: stuff not in containment, they can vent and destroy parts of themselves or
: even the whole ring if necessary to stop the spread of the Flood.
: Considering the Flood came from outside the galaxy the Forerunners decided
: better to keep some around for study and possibly find a solution rather
: than kill it all and be back to square one if the Flood returned.

Spoilers below if you haven't read the Forerunner trilogy...

I don't remember the exact quote, but in Halo 1 during the library level as you're fighting with wave after wave of flood, 343 Guilty Spark keeps talking about various aspects of the flood, its containment and storage on the ring, and your armor and weaponry. I remember him commenting about how they were kept on the ring for study. The Covenant are referred to by him as meddlers as well, as they are the ones who let the flood out on installation 04.

Also, in the Forerunner trilogy of books, humanity was seen as having had a method of dealing with the flood. The Forerunners thought that humanity had once defeated the flood and driven them back, only to be defeated by the Forerunners and de-evolved into primative life forms. It's unclear if humanity actually did defeat the flood in the books, but that was the going theory as far as the Forerunners thought of humanity. They designated humanity to be reclaimers on the chance that humanity would one day be able to defeat the flood again, since the Forerunners were never able to defeat the flood themselves. They kept the flood on the rings hoping to one day come up with a method of defeating the flood as a back-up plan, I think.