I am not going to comment on the matter, it seems pretty understood that the Flood had to have lived, in some shape or form, but Bungie did say they were done with the Halo Trilogy. I think that is their way of being sneaky, because the Halo Trilogy is over, but they can still expand on the series, like Lord of the RIngs, and The Silmarillion, and Unfinished Tales.
Oh and Here;s a link that I go to often for Halo stories and just general information:
http://blog.ascendantjustice.com/
They have tons of blogs that are just very analyzed parts of the Halo series.
http://blog.ascendantjustice.com/halo-3/the-terminals/a-voice-from-the-tomb-i/
That section^^^ talks about the Forerunners b4 they disappeared and it talks a lot about the Flood. They found their information from the Halo 3 Terminals in that section, so it is all true.