Realistically, unless Jon is a total bastard, he'd have to do something.
First of all, just because the main characters adjusted, the world doesn't revolve around main characters. There may be people who are the equivalent of transsexuals ("I'm a human stuck in a giraffe's body"), or who are even actual transsexuals since their mind doesn't match their new body, and who may never adjust. Some people may "adjust" but only by making the best of a bad situation. And even for those people who've really adjusted, there's the question of whether they only adjusted because of the magic, and if so, whether adjusting because of magic should "count". If you turn someone into a frog and magically make them like it, that doesn't excuse you from being morally obliged to change them back, since they aren't really freely choosing to stay a frog, it's the magic doing it.
Second, not every transformation is convenient. Some people are rooted to the ground. Some people can't speak normally. Some people can only live well in inconvenient environments such as in the ocean. Some people weigh a ton and can't even ride buses, let alone drive cars (I haven't been following all of Iridescent Sun, so forgive me if someone wrote a weight limit into canon). Some people don't have hands or fingers. Some people have very inconvenient dietary habits. Despite technicalities about it being natural for their species, Jon has basically created hundreds of millions of handicapped people, and he owes it to them to change them back; the fact that some of them have the equivalent of wheelchair access ramps isn't an excuse not to.
Third, in most stories the transformation is done by villains or by accident or done to people who are in a position to give consent. And the rest are typically stories where the plot is a thin excuse for the transformation and we're not supposed to take them all that seriously. Iridescent Sun is none of those, and transforming someone's body without their consent is violating them on a very personal level, and the violation exists as long as they are transformed. You just can't have a serious story where someone who isn't a megalomaniac transformed everyone in the world and thinks it's perfectly okay for it to stay that way.
