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A story about wishes ending with a "perfect" wish that fixes things for a happy ending is the standard trope. Her particular wish isn't anything special for an example of that trope.
Homura doesn't munchkin anything. She has two or three absurdly powerful abilities, that she uses in the obvious way to use those powers, with which she brute-forces any problem she faces. She has a bit of a learning curve where she starts off pathetically incompetent, but that doesn't make her a hyperrational munchkin type, it makes her a protagonist.
It uses the alien utilitarianism thing to simultaneously point out utilitarianism as obviously right and shit all over it and say humans can't be utilitarians. So, yes, deliberately morally ambiguous, but not in a smart way.