Someone might have covered this though, a key reason Flood defeated the Covenant or the Forerunners is that they attacked in small groups, allowing the Flood to overrun there lines. Look back in Halo or Halo 2 and tell me if you see more than 10 guys attempt to 'quarantine' the flood.
So basically, if the Covenant had about 50 ghosts or so and close airsupport, they could probably repel any flood attack. But ya see, the Zerg also attack en masse, and as many of the other guys have said before, are reasonably stronger than flood units. /end rant.
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