If Harry's going to end the world, surely a more likely way -- especially given the author's known interests and opinions -- is by bringing about the magical world's equivalent of a Singularity? MoR!Harry is on record (albeit not in chapters 1-3) as wanting to take over the world and, er, optimize it. There are suggestions elsewhere that terrible things have happened in the past on account of over-powerful magic. (Again, not in chapters 1-3.) Centaurs and other purveyors of prophecy might dread this even if the singularity ends up being a good one, because it would be a point beyond which they wouldn't be able to see anything.

Another possibility -- which again could reasonably be said to be heavily foreshadowed, if it comes to pass, but not in the first few chapters: Harry is somehow going to put an end to magic. (He wants to do away with Azkaban by any means possible, no matter how drastic. He's already explicitly considered the question of which side he'd be on if it came down to muggles versus wizards, and decided for the muggles.)

I don't assign a terribly high probability to either of these. There seems to be no shortage of mutually incompatible outcomes with a certain degree of foreshadowing, and if there's a good way to decide between them then I haven't spotted it yet.