Why does a molecular sieve work for gas separation?
I have seen finer zeolites but this one does not seem as coarse as you sounded it. Consider it again, likewise in fractional distillation, there will be some molecules with never being an equilibrium with another phase. However, much more of them will go through zeolites and with the passage of each unit distance and time, you will have more of the compound you want to get and less of the redundant one. If your column is enough long and zeolites are sufficiently fine and ordered, it will be a good purifier. 

Try to visualize it in more detail, while some molecules try to pass through the cavities between zeolites, other molecules will be forced to collide and travel through directly zeolites.