Except that it does apply in this case. If your director can keep away from close foreground shots, you don't get this problem. The angles between the eyes and the focusing power of the lens differ minimally once you get several meters away on out to infinity. From several meters to your nose, yes, heaps of variance is required and it would be very hard to do.
This is just Ebert being an idiot and saying "This is my opinion, stated as fact, case closed. I won't enter into any discussion because I might be wrong", just like he said when he declared video games weren't art. It is /profoundly/ unscientific to dismiss something as unfactual simply because you don't like it.
Back in the day, my honours degree was specifically involved in investigating ocular vergence (research jargon as 'angle between the eyes' as opposed to the /action/ of converging), comparing between a collimated image (= light coming to the eye in 'parallel' - from a military helicoptor pilot's HUD) and a real image (= light coming in 'non-parallel') displayed at 3m. At that distance there is already not much difference between focusing or vergence at 3m and at infinity (ie collimated), though discrepancies slightly increase as you move towards the periphery of your vision, though this may have been an artifact of the presentation of the HUD.
I am not an expert in 3D and don't proclaim it to be 'there yet'. I do think that 3D is doable if the director stops the temptation of the 'power' closeup to showoff the 3D. So yeah, I think within constraints, 3D is doable. All film has constraints though, and those constraints are gradually eroded over time - such as night-time filming. Fifty years ago we would have heard Ebert proclaiming that it's impossible to film in natural light at night because film needs a certain amount of light, case closed, yet we've seen some amazing cameras arrive recently that can film at night using natural light.
EDIT: Another example constraint is limiting yourself to a 'viewing box' - you can't turn your head for a full view of the scene in a movie. You're limited to a particular forced view. Despite this rather incredibly limiting constraint, film has managed to do some pretty amazing stuff.