Using dead corpses as hosts aside, they are not at all zombies. They're one of the most important elements in the story. Everything that has happened is pretty much hinged around their existence, from the dawn of the Precursors and the Forerunners up to the recent Human/Covenant War. The Gravemind remains one of the most fascinating characters in the series, and I highly doubt that he is dead.
There are still presumably six Halo rings left with Flood on them in some capacity, plus probably more Flood out in the far end of the galaxy. There's a lot of Forerunner installations that we have yet to discover. With the resurgence of the Forerunners in the "modern" day story, the Flood surely can't be too far behind.