I guess I can see for the sake of completeness that someone would want that. However, even if it was on the disc, I'd never watch it so I couldn't care less if the edited version never saw the light of day again.
"...most likely never be seen in HD clarity"? Just because it didn't come out in this set doesn't mean that it won't ever come out or be released solo. Plus, there's always the next time they release the Kubrick movies again in 4 or so years.
That's probably going to be my move but I'll still pick up Eyes Wide Shut since it's uncut. My buddy will either rent or buy a couple of these so I'll get to see them sooner rather than later anyway. :)