I have a theory on how the Flood are in the Campaign but they still don`t know about them. The Spirit of Fire gets its radar jammed or damaged so they can`t transmit then after they encounter the Flood they can`t leave because they have troops on the Ground the Covenant reinforcements show and obliterate thus killing it and her crew ending the game and allowing the Halo Storyline to be un-phased. For my Full better Theory follow link.
They will have to include the flood in Halo wars. The human and elites are not only fighting each other, but they are also fighting the flood.