This has been somewhat overstated. While Moore did approve of the show adapting the story beforehand, he has never given his opinion of the result, and it is unknown if he has ever even seen it.
Word of God: J.M. Dematteis, writer of the animated adaptation:
I don't think he'd be happier on Krypton. It's just that Superman never really knew Krypton and had a profound longing to experience that part of his history. Krypton is part of him but Earth, I think, is a bigger part.
What Could Have Been: There are some rumors going around that the story was supposed to be about Martian Manhunter. If so, then the protagonist's characterization as an alien who wants his perfect life to be on his revitalized home planet makes a lot of sense.