With the destruction of The Halo Ring. The Flood on both that ring and Installation 04 were wiped out. Yet there are the other installations, possibly holding more test subjects of the flood.
However, in the Eyes of the UNSC; its only been 3 years since mankind was almost wiped out by the flood. Their New Spartan IV’s will need to learn how to fight them if the situation ever were to repeat itself.
It would make the most sense to hear about the Flood in story-mode as canon only, instead of fighting them. As everyone would probably be more casual as to unleash them once again.
Also, There still is the “Infection” Game-type in the War Games Simulator.
It would hard for the UNSC to not be prepared, so In their simulations, Flood would most likely be an enemy prepared for.
Until more information is released about Halo 4’s Infection mode, OR the campaigns of the new trilogy are released, Well never know.
But unlike Halo Reach, It is definitely possible.