The Flood are still in the Galaxy. Flood samples were stored on Installation - 04 so it's possible that more samples were stored on the rest of the Halo Rings, which can be released in similar ways to the "Screw-up" that happened to the Covenant in Halo: CE.
For example, on Installation - 07 it seems that it is covered in Flood biomass. It is possible that the Flood escaped Quarantine and managed to infest the Ring.
Though it is also possible that the surface is just harsh, and not infested: like the surface of Venus.
Plus there are more then likely rogue Flood spores scattered everywhere. I'm not sure if a Spore can survive the vacuum of space, but... Well to sum it up I'll quote that Hing Head Elite from Halo 2 and 3 ~ "A single Spore can destroy an entire Species" or something like that.
Anyway I think that the Flood will return. I know that everyone says that they've had enough... and I think that's pretty stupid. I loved the Flood, and Flood levels. I would welcome a return.
I would discuss about The Forerunners, and Ur-Didact about not being gone, but I'm too lazy.