This article contains major spoilers for Saya no Uta, gratuitous re-interpretation of canon, and probably a lot of words. Be warned.
When Saya no Uta first started showing its true colors – when Urobuchi first decided to throw a spanner of Lovecraft into a work that had been entirely plausible as a sci-fi story – I was a bit disappointed. Sure, the old L-C is cool and all, but the whole going mad from the revelation kind of thing never felt right to me. And honestly, don’t you think the “true” ending is kind of unsatisfactory? The aftermath is certainly implied to be a horror by the tone of the novel, but we’re never really shown its effects in detail to let us judge by ourselves. Let me fix that, and give you one heaven of a take.
But really though, scale back the layers and think of any magic you see as merely technology you cannot comprehend. How did Ougai contact Saya? Through some kind of communication unknown to current science, accessed by the occult artifacts and knowledge he gathers. The transport of Saya to Earth? Through that same network. Her home planet’s motivation? Efficient spreading of their superior culture throughout the universe – the ends very much justifying the means for the dull, foolish population of the planet we live on.
Let us ponder the method: detecting an occult signal is a surefire sign of intelligence, which indicates habitability by an intelligent species; genetic modification of the host species ensures ability to keep unique environmental modifications (though terraforming also occurs). It is also possible that teleportation is only possible through occult conduits, and Transformer probes such as Saya can only be sent if the other side invites them.
Modification is also significantly more humane than another viable choice: eradication and founding of a new colony. While it can be argued that some of the humans transformed by the gene-modifying spores released by Saya in the good ending would consider themselves to have “died”, and the transformation process is likely to be distressing (though likely tempered by its relative rapidity in most locales as well as communal development), I cannot agree that the elimination of 7 billion humans through some means is preferable.
As for any generations birthed after transformation, there should be no argument that them being of Sayan heritage is preferable to them being human by any sane measure. From Ougai’s notes as well as her own feats, Saya’s intelligence and ability to learn is markedly superhuman. Saya’s species is also sure to be able to create supertechnology far beyond the reach of our current civilization if they are able to precisely teleport anything.
There’s only one conclusion: Saya no Uta has only one good ending, and it’s the one where humanity is turned into tentacle monsters from beyond the void. The two others are horrible losses of potential, and we can only hope that a world-conquering probe such as Saya will be summoned to Earth once more, this time to succeed.