To me it was about Superman trusting people and giving them second chances even when he could just beat them up.
I'm sure that the idea was that "Superman technically didn't steal anything, he just synthesized it", but it rises another question - why he didn't do it earlier? Unless I missed it, these crystals are not "new thing" since UP workers knew what they are so they were present in other planets as well, but Superman probably didn't feel like making them irrelevant since they were on friendly planets? And whole idea that Lex didn't do any geological research on his planet (they were basically on surface!) is mind boggling.
So now planet is still isolated, is still ran by Lex and doesn't have any natural resources. But hey, United Planets solved their energy problems!