I'm still in the camp that believes that the problem is one that originates with the Ancients and their Creation magic affecting the planet in a negative way that none of them could have foreseen. The main reason I believe this has to do with the side-story about the phoenix and its accidental ensouling. Emet-Selch is the foremost authority on the Lifestream and the transition of souls to and from it, and even he was befuddled by the phenomenon. The Phoenix, for its part, was clearly insane and in pain. I feel that this was a hint that something was very wrong with the Lifestream as a whole, and they simply weren't able to puzzle out the problem in time. (Or, for that matter, even try; they simply decided to mercy-kill the thing and put the whole matter behind them.)
I'm ready to believe that the story had little or nothing to do with the eventual Sound-driven cataclysm. It may simply have been a glimpse into the mindset of Emet and the other Ancients, highlighting their unmalicious callousness when it came to lesser beings (a callousness which would later be inflated to the point where they were willing to do what they did to usher in the Rejoinings). For now, though, I believe that the Phoenix episode was a hint at the origins of the Sound and the End of Days, and how even the greatest among the minds of the Ancients failed to recognize the threat before it was too late.
Creation magic was an ability possessed by the Ancients that was as ingrained to them as breathing, and I think that normal use of it should not have posed any kind of threat to the planet. What we saw of Amaraut, though, indicated that they had made both art and science out of the use of Creation magic, pushing the boundaries of what it could do. That, I think, was what began to corrupt the Lifestream and lead to the disaster that followed. Giant space flea is another possibility, to be sure, but it's my second choice.
Eventually, yeah, they turned to these desperate plans. Earlier on, though, it appears as though they were less concerned about it, hence the "debate" among the Ancient NPCs about whether Amaurot should go to the aid of the far-off suffering cities or not. Once the problem was on their doorstep, you're right, they started thinking long and deep aobut what to do. (At least, as long and deep as they could with monsters literally springing out of their heads left and right and fire falling from the sky.)