Yes, that is true. I've tried to always be grey in terms of outright morality. A lot of stories do the same to me, as well as certain webcomics... We had trouble when we brought religion into the last story, bringing politics was always going to be sticky... (We went beyond sex ages ago)
I think using a story for political means destroys the story. We are all biased to what we want to see. Even how the basic 'I turned into a girl am I happy or sad' can become very political. I've tried to be balanced about it.
Regarding some of your points:
I suspect that in the IS world, there is a wish in place that prevents government or military from interfering with the wisher. that makes a lot of sense, and we might explore how it came about. This is obviously not something that is known to any of the characters so was never brought up.
We have addressed Jon's actions in the past, and concluded that he was not entirely responsible. There is an aspect of 'fate' in this world, though he is still accountable for the actual results of the wish.
The wish 'did' save the universe, which was always in a state of 'doom' regardless of a wish or not being made. That's why fate gave Jon a world changing wish in the first place. Jon has also tried to fix the wish so that not everyone is changed, only those that are 'better off' remain transformed... and its a lot rarer now to go from human to a changed state.
Third, Jon- as Jen, is being trailed, in the far future, for not 'fixing' the world outright. We see glimpses of it now and then in the form of a game of chess. It is not a trial as we know it, and the punishment might not be to our understanding either. But Jen will see everything she has done, and the morality of it all thrown at her. She'll be held to account.
On Lucas, I acknowledge her views appear extreme. But I'm open to the possibility it might change. I think the General has shown many good points early on, and hopefully the two interactions will bring balance. Much like the Doctor and the Brigadier.
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Finally, politics in a changed world would change to adapt. We've tried to keep an optimistic beat to it though. For instance, there is less antibiotic resistance to worry about, due to smaller populations of individual species types being so spread out. In a few generations, its even less likely anyone will realise it was just a human world once.
