The Kryptonian environment was Superman's weakness (or kryptonite) which was a subtlety (i.e. a hidden message or Easter egg).
I can't agree that the Kryptonian environment is damaging is an Easter Egg. I'd say it's more likely to be foreshadowing of the damage actual Kryptonite will do him in the potential sequels. Plus, I think Easter Eggs have to little, decorative things, and this was too big a part of the plot.