Yes, convenient exceptions are made when it's the 'bad guys' being subjected to such transformations though if someone turned Alisae into a tree I daresay the Scions would seek to do everything possible to try to reverse it. In the event that they couldn't, they'd be incredibly angry!

Of course given how the protagonists are comfort characters who cannot possibly be meaningfully harmed in any way then it's unlikely we'd be able to see such an experiment play out. How unfortunate.

It's less so the act itself so much as the double standard. During Stormblood, the Eorzean Alliance shifted from the 'defender' to the 'aggressor' but they certainly didn't just shrug and say 'they were just defending themselves' whenever Garlean experimentation/body horror was put into play. Fae body horror and transformation is little different, really.