There's also the option of having it not magically transform so violently, right? I mean, we've seen this in zelda games with ALTTP's Lost Woods, and the Deku Swamp from Majora's mask, where they kind of transformed, but really they just became easier to traverse. Still the same basic layout, but obstacles such as poison, fog, enemies, whatever went away, and friendly NPCs came in. Not necessarily a whole town full of them.
Perhaps we have a maze-like, foggy marsh that is difficult to traverse and full of enemies, and is so maze like that it's like the lost woods in OoT where you can get teleported out by being lost. But after beating the forest temple, becomes more stable, the fog lifts, and a few fishermen move in or something smaller than a whole town?
That's just an idea, and my opinion.