Jon really doesn't have the right to say "of course she would desire to be changed back, but is it really good for her?" He's not her, or her parent. He shouldn't make this sort of decision for another person no matter how good he believes it to be; personal autonomy matters. Sure you could write a story where someone wants to be changed back, gets changed back, and eventually regrets it, but that isn't something Jon can use in any moral calculation. Just like with abortion, it's their body, so it's their choice--Jon must not make it for them (unless magic keeps them from making free choices--but that would lead to people not wanting to change back and Jon having to change them back anyway, not the other way around.)
(It might be interesting if Jon decides that for children, their parents get to decide whether they should be changed back. I'm inclined to reject this idea for older children, for the same reason that I don't want parents to decide whether their daughter can get an abortion, but it's at least not blatantly evil.)
And someone who is rooted to one spot, or has no fingers (without something that compensates like telekinesis) is, in fact, handicapped by any reasonable standard, and changing them into that condition and then deliberately refusing to change them back is horrible, regardless of whether it's natural for their species. The fact that we can remake society to take into account people who are immobile no more excuses it than the fact that we can make wheelchair ramps would excuse wishing away someone's legs and refusing to restore them.
