Several points to that:
1) the community has never advocated, accepted, or encouraged those kinds of mods in the past (mods that added BtS concepts to vanilla, for instance), why would we start now? I doubt CFC would host the mod, since it would violate the code of conduct. If the major fan sites won't host it and Steam won't host it, it's pretty much a non-issue for them. It won't reach that many civvers.
2) the only thing about the civs (any of them) that would be protected under copyright would be the graphics (leader, unit, ub, etc...) - the data itself (flavors, stats, effects, names, etc...) are not - just like you cannot copyright a recipe, you cannot protect numbers. If someone puts out a Babylon civ with different graphics, why would Firaxis care? It won't be their Babylon - and if the modder is going to go through all the trouble of creating new leader animations, who's to say they'll even want to make it look the same? As a modder, if your art & animations are as good as Firaxis's, you'll probably want to make different choices regarding costume, setting, and mannerisms anyway.
3) If they have no plans to continue to sell Babylon (individually) after release, they aren't really losing anything. . .