I always like thinking that there was just a large amount of Infection forms from 2401's inability to fully quarantine the Flood, and that the Covies and Humans sent a force that was not expecting a Flood force of that mass and simply got assimilated. You gotta remember that that the Humans already got a small force past the wall in the first place, which is why they were in front of Thel anyway, and that after the shield went down, both the Humans and the Covenant could've easily sent for some heavy ordinance without being aware of the gigantic Flood force awaiting them. And BOTH of them really wanted the Index. We saw a lot of heavy ordinance such as tanks and rockets being assimilated and used by the Flood in Quarantine Zone. Aside from reports from Regret during the catastrophe in attempting to get that Forerunner fleet in Halo Wars and the great Battle of Installation 04, there was pretty scarce intel on the Flood. I doubt any side knew what was gonna happen or was properly prepared to combat it.