I agree, I have no problems with a villain who might not be all that villainous, just "an antagonist". To them, a helpless heir who cannnot ascend to the throne is just as good as a dead one. Heck, imagine a villain who uses this kind of polymorph magic to show enemies mercy instead of murdering them!
"You see, Princess, the aristocracy and the monarchy are the problems with this world. I propose to replace them all with a meritocracy, where the fit rule, and no one has privilege just because of their bloodline. But as long as you live, some will see you as a symbol, and wish to overthrow my new order, and elevate you to a Monarch, whether you would be a good and just ruler or a despot. No tower, no prison, no dungeon I have would stop that.
It only ends with your death...however, I have an alternative solution. My Wizard possesses a powerful magical device that can transform you into a small child. Too young to ascend to the throne- but you would be alive, and live for a very, very long time. Further, I will ensure you will be taken care of and live comfortably...at least until someone succeeds me.
So what will it be? Life or death?"