Nye isn't stupid, he's thought about the implications of this debate. He's already talked about the promotion of the debate as a leveling effect of the two approaches, when really they are nowhere similar. (Creation Mythology and Scientific Inquiry).
However, I think if Nye plays his cards right, he'll not fall into the trap of a tit-for-tat banter of each little Creationist pseudo-doubt. Instead, he'll address the general sociology of the subject: The Christian religion is just one of dozens of creation myths, popular in certain places of the world at this time in history. It simply cannot admit it is wrong, although it has been proven wrong many times and simply abandoned those historical issues (Copernicus onward, for just a few examples). Additionally, there are still the hangups in Christianity with gender (both women and gays) as lesser actors on the stage. Combined with the peculiar Politically-rightward stance in the US, defining their positions on the environment, poverty and interventionism - Christianity cannot explain many parts of the modern world well, let alone creation.
Nye could also simply state that there are too many religions to include them all in an Origins class, and all of them arrive with only scriptural evidence that it's best left to a comparative-studies class on mythologies. Which is exactly where they are today.
Also, if everyone started empirical scientific exploration over again (really, we do this all the time in teaching) - the same models would be arrived at - simply because the models fit the observations. They aren't dictated from any secret cabal, exactly opposite the Christian method. Nye can do this, as well as any of us. The evolutionary discrepancies Ham will blubber on about are not worth the time, but this entire use of one religion to define all things in the universe can easily be made to look silly.