Actually, I believe Discord only arrived in Equestria after Princess Celestia and Luna were coronated. The only enemy described in pre-equestrian history was a Windigo. And according to Hearth's Warming Eve, Unicorns already had to raise the sun and moon by this time.
As far as explaining the origin of ponykind and their role in the world, I'm sadly doubtful. It'd be a fascinating topic for movie or a finale, but this seems like a cutie mark kind of mystery. You know what I mean?