The main requirement for the hole is that it's small enough that (with high enough probability) only at most one or a handful of molecules will make its way through.
And that size is completely independent of the size of your molecules, and only depends on how many there are per unit volume. There's a lot of 'empty space' between molecules in a gas.
> In the middle of the divider was a tiny gate, just large enough to admit one molecule of gas.
Still, that's quite a small hole relatively speaking. So you'd have to be fairly precise about both position and velocity. Potentially more than is allowed by Plank's constant. I dunno though, this isn't one of the counterarguments in the Wikipedia page, so probably you're right.
So all in all, a classic description would work reasonably well. (Remember that quantum uncertainty is related more to de Boglie wavelength than physical size.)
