The testing and containment facilites used to be off the rings, per a discussion that takes place in Halo 2 with regards to the setting of the Arbiter levels (when he's going after the Heretic).
Seems to ME you'd want your failsafe kept as close to the problem as possible.
This breach of containment was still considered contained, and therefore not a threat outside of that ring. It called for securty, and security never came.
You also don't want things being triggered to go off BEFORE you get a change to evacuate the galaxy first. They probably wanted to avoid an automated genocide switch hooked up to a motion sensor.
and intended to be back to take care of issues like this.
Granted, after 1000 years or so, the system should have determined there was a problem with the lack of responce, but it's not quite the same as an out of control infestation. In theory, even if the ring was absolutely swamped by what it contained.. there's no way to get off of it... therefore it is still a contained threat. Perhaps it sent out a warning flare of sorts, but as long as there were no other rings in this kind of situation, there's no real risk of galaxy infestation.
As for why they didn't just wipe out the flood when they had the chance? "All life is precious" So they wiped out everything EXCEPT for the DNA codes and stuff stored and cateloged on the indexes, which would be considered perhaps "life with insuficient biomass to sustain flood".
(as per the bestariums opening admonishment.. "don't use this information to revive anything you find in here please")
Otherwise they'd be no better than the threat they fought off and would only offer death to all living things in an entire galaxy. GRANTED that distinction is small.. but what would be the point of their actions otherwise? "WHEW! the flood is extinct, but so is everything else!"
They intended to wipe the slate clean, restart the galaxy, and even "reseed" it with forms that could "reclaim" the galaxy for themselves using the remaining lifeforms as "stock" to be altered genetically until the resemble the cateloged species. They probably figured that by keeping the flood under observation and study, if any MORE entered the regrowing galaxy, the inhabitants of the galaxy (and Forerunner AIs) may have had more time to come up with a better plan for defeating them.
But.. I have brain busting "proof" for you.
Ever wonder how "early man" watched the ark portal being built in that comic series, if the last firing of the rings ocurred so long ago? And why the Cradle (origin) of human life is beleived to be in a region close by?
We were reseeded by somethng similar to sentinels.. which is why the one forerunners was glad she'd catelogued us before the firing of the rings. So that we could come back, and not be lost forever. Early man witnessed the sentinels handing us the reigns to the Halo installations.
*update*
In fact.. who's to say that the forerunners actually built the arks, and they weren't built by the precursors? I say arks.. because who's to say the "old events" even took place in THIS galaxy? Perhaps the Forerunners inherited the knowledge of them and even improved upon them Maybe there's an ark in all the neighboring galaxies as well? Apparently since the "forerunners" had such a grasp of this galaxy, it would suggest that they had been to neighboring ones as well.. (much like our "ark" is outside of this galaxy) Perhaps our "forerunners" were reclaimers themselves? to reclaim the galaxy once it was purged. Maybe we ran into the flood a little early this time.. prior to being given all the knowledge we were supposed to have once we come across the rings? It would certainly explain the Monitors being surprised at our lack of knowledge on the subject.
oops.. I better stop.. I think I pulled something..