It's pretty much separate licensing that's the issue to getting a re-release of pretty much anything.
Netherrealm by the way it was described in a rapid fire interview with Ed Boon was that they simply ask companies if they can use certain characters as guest spots. It's pretty much up to the license holder if they want to have their I.P get blown apart or maimed in an MK game and they go from there. Meaning that regardless of it being WB or not, the decision to get Alien and Predator into MK was Fox's decision when Netherrealm asked.
I don't believe Fox or Netherrealm owns those specific instances of the characters and that they would have to renegotiate if they wanted to use them again. That being said, we don't know what that contract looked like, but I'd imagine it was only for that game.