Saa's goal was to use Elizabeth in order to destroy the frogs and usher in a new age IIRC. Something like that at least. He said that millions would die in the process of creating this 'new world'. As far as I'm concerned, that's exactly what happened in King of Fear. Elizabeth used her power (all of it) to wipe out all the frogs, yet she destroyed Indonesia in the process. Millions died.
This new world however. This new world has Ogdru Hem sneaking into the world, bit by bit, and causing mass death. If the frogs had won, wouldn't the same thing be happening (though maybe as an invasion as opposed to gradually slipping through the holes)? The frogs and the Black Flame also wished for a new era, most likely the same new era that's been trying to be achieved by Rasputin, Von Klempt and Zinco since the start of the series. The era of the frog race, the final race of man.
Merman Saa seemed to be aiming for a new era also, except one involving Vril and Hyperborea as opposed to the Ogdru Jahad. Saa may have been an antagonist but it seems he had genuinely good intentions.
Or perhaps, the world of the BPRD is still in the process of changing into the new world. Millions are still dying in Houston and Britain. Perhaps Saa's prophecy is still in process?
It's simply impossible to theorise what might be happening, but what do you think is currently happening in the BPRD regarding this? I've not read beyond Gods and Monsters so if it's been explained since then please use spoiler tags.