Board Thread:Warhammer 40k General Discussion/@comment-92.97.77.182-20130321145115/@comment-3186669-20141003133225

There's the problem that, although at the end of Legion, the Alphas seem to have sided with Chaos (to ensure the ongoing survival of the galaxy), they didn't do it wholeheartedly. They allowed Loyalist forces to escape the Istvaan sector, bolstering the Loyalist forces when they could have crippled them further. There's a few other events in other short stories where there are shown to assist Loyal forces too.

So while they outwardly appear to have gone to Chaos, they didn't do it completely. That's why the second vision (of humanity having a slow decline in the event of the Emperor winning) is the one that came true. If they had completely given themselves to Horus, there would have been less support on Terra for the Emperor, and it's quite possible that the war would have swung in Horus's side, as he wouldn't have needed to make the last-ditch effort in lowering his ship's shields to lure the Emperor on board.