...to turn people into trees?
We don't know enough about puppets yet. Were they people/creatures controlled by the puppetmaster or inanimate constructs animated by the puppetmaster?
It's been pretty well established that the puppets were inanimate armatures and/or war machines given life by the Puppetmancer. It was Suzocon that was working on meat puppets. But those needed a soul, so he decided to try and make a blank slate. To program in his Miyo meat puppet how he saw fit.
Also there was one kami in this world that might have been able to turn things into trees: Ayal and his Dryads. And he was the first corrupted kami the main chars came across, and the only one so far they've managed to defeat. The Dryads still go bonkers if they even so much as sniff something that may be a puppet.
Things that make you go hmmm...