Jumping into this conversation late in the game as a DL afficionado.
But, again, I have to ask, who considers the Cataclysm to be a good act? It might have been the right one (and we can argue that for a long, long time) but, AFAIK, no one ever calls it a good act. No one claims that the Towers of High Sorcery are good. Necessary, but, good? I don't think that's ever even suggested.
So free will is just another thing that does not justify the "good" gods' evil actions.
Their duty us also cosmic in scale the fate of a comparatively few doesn't matter.
DL "good" and "evil" has very little to do with the morality of mortals. It has to do with the existence of the cosmos, which despite the will of the Highgod, is a very fragile thing. Evil consumes but also provides conflict which can strengthen. Good furthers life but can stagnate without challenge. Neutrality is all about free will (e.g. commerce and creation provide weapons that can kill, but life can adapt to withstand). Chaos is the antithesis of existence but also, in moderated doses, an essential feature to provide variety (pure chaos might create gnomes that can't breathe air and instantly die whereas moderated chaos introduced into the world makes for an entirely new, fantastic form of life).
So, the Cataclysm shouldn't be viewed on the scales of mortal justice. "Good" (life) had gone too far because it was only supporting one form of life to the eventual extinction of others (humans were, without killing and in the name of good, delegating other races to small corners of the world). Stagnation was imminent. On a cosmic scale, the gods stepped in to reset the scales. Conflict would strengthen and diversify. If not for the Cataclysm, the races of elves, kender, and ogres were on their way out.
In doing so, the gawds of DL in some ways violated the neutrality tenet of "free will," but neutrality was never about the idea free will would lead to pure balance on its own. And, as odd as it might sound, the DL gods of good didn't gift "free will" to mortals. They're not about free will at all. If the gods of good were the only beings writing the laws of existence, everything would live forever unchanging. Hence, the elves were their creation. Even so, with the Cataclysm, the gods of good saw life diminishing if allowed to continue on the course it was. The DL gods aren't human and they don't have free will. They exist according to their nature, and that nature was to keep the cosmos going. For once in the existence of Krynn, all were in agreement what needed to be done.
That said, it's a wonderfully diverse world because of this type of complexity (e.g. understanding why the gods left is THE impetus behind the novels and motivation to play the original modules), and I'm pretty sure WOTC is going to completely pass on messing with anything metaphysical or philosophical. That's fine. We can figure that out at our individual game tables using our forums and AD&D material to make it unique.