I think that there are possibly Forerunners left, but somewhere outside of the known galaxy. I haven't read all of Cryptum yet, but so far where I'm up to, it's been suggested that the Builders may have kept many secrets from the rest of them, and possibly began to expand outside of the Galactic perimeter.
After all, we do find the Ark beyond the rim. It would make sense that when the Halo array was activated to cleanse the Flood infection, that it would have been executed from that location. Thus, whoever was responsible for the activation, however few or many, would have used the Ark as a base to launch an expedition out of our known galaxy toward a more desirable, Flood free location, to begin rebuilding the empire.
I might be wrong, but it's just an idea.
[Edited on 09.07.2011 10:01 PM PDT]