I'm sure DC Comics advised NRS to make Zod an actual playable DLC character because of Man of Steel; they wouldn't just want him to be a skin when they have such a film coming out. I really don't doubt him being in the game at all. Even before the rumored list came out, I thought he had a big chance of being DLC. If there was anyone I doubted the most it was Batgirl - out of the actual DC characters that were rumored at least. Personally, I can see how Zod would be quite different from Superman gameplay-wise. He has much more of a militaristic theme than Superman. This was the same exact issue with Batgirl and Batman - similar gadgets and theme.
But there are many "clone" characters in general that are written to have the same powers or abilities, but in a fighting game, you can technically make anyone play differently by changing mechanics and animations. You could say that everyone in Tekken is the same just because they only punch and kick, but we all know there's much more to it than that. Especially with a game like Injustice, where there are character powers and meter burn variants of special moves, there are so many mechanics that can be designed to make a character play extremely unique. Animations alone can change the whole feel of a character, and there's a multitude of other things NRS can design.