That was an interesting read, but I still think it supports the idea that you'd want to stop down more on say a 5d mk ii than on a 5d. What it does say is that if diffraction is your only criteria you'd be misguided buying a 5d over a 5d mkii just because it has larger pixels. Admittedly I just woke up, so I'm still a bit out of it, and if I missed something, I apologize. But here's my conclusion anyway:
Instead of thinking about absolute resolution I'd think about it terms of lost resolution compared to that absolute, something you're probably interested in if you upgraded from a 5d to a 5d mk ii.
Let's imagine a 5d and a 5d mkii taking the same picture at f/16. At f/16 the 5d is just beginning to be diffraction limited and you're probably going to get most of the resolution the sensor can render. The 5d mk ii, having smaller pixels, has already begun to feel the effects of diffraction. Based on that article it hasn't lost all of its resolution, but it has lost some.
Maybe the mk ii is down to 16 MP from 21.1 (I made the 16 number up to demonstrate the idea; I have no idea what the real number is other than it being less that 21.1). That's still more than the 5d's original 12, so as the article suggests, at the same aperture the smaller photo-sites are at worst equal to the larger ones, but never worse.
But, there is some resolution lost over the maximum 21.1 you'd have if the camera wasn't being diffraction limited. While that lost resolution gives you no incentive to change over to a 5d since the absolute resolution is still higher it does give the 5d mk ii more incentive to stop down than the 5d shooter in order to maximize resolution.
My conclusion is that while the OP can shoot at f/16 and know that he's getting a higher resolution image than if he were shooting on a 5d, there's still a reason for him to want to user a larger aperture if that option is available.
Perhaps the real world loss of resolution isn't that significant. I'd imagine that the lens quality and shooting technique would probably limit resolution before diffraction (especially at f/16, which may have been your original point), so this conversation probably doesn't matter. I'm also curious about the article's claim that a proper algorithm can be applied post shoot to remove diffraction. I don't understand how that would work, but it sounds interesting.