Really, that's the only option?
Yep. That's the only solution.
You can't use the crucible to force them to re-combine somehow?
I mean, if you could undo the magic of an Devil then like half the plotlines in the game would be rendered moot...
And how is just one remaining rat sufficient to reconstitute the human?
The magic splits Lyrthindor's soul among the rats. Killing them releases that part of his soul and that can recoalesce into his human form.
Anyway, 5 more rats immediately attacked. What? How were they not sucked into the recombining person?
At a guess I'd say not ALL the rats in the temple are parts of Lyrthindor. Some of the rats might just be regular rats (Whom have BG3 related telepathy to know when you've started a fight with their friend...)