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It wasn't overtly confirmed, but I thought it was very clearly the case in Halo CE and Halo 2's plots, especially the end of Halo 2. Although there's nothing in the first two games that contradicts the new canon, it doesn't fit thematically with the Forerunners' story, IMO. And it ruins the SPARTAN: FLOOD parallels that existed.
The recent revelation about the Flood's true origins just reeks of the writers doing a 180 to create some kind of surprise. Reminds me of Sheppard Book's true origins in Firefly.