I consider changes to OAR, with very few exceptions, heinous as they are defacing the original work. If the original is readily available, I don't make a fuss as I will not look at the altered version more than once (usually to see if there is any content worth seeing that's not at all in the original--like a different cut). If the director approves the new AR, I respect the right of the creator to tinker with his work--whether I like the final result or not. In the case of Kubrick, I have had debates with friends over his choices in home release AR--defending his right to change his own work (even though I much prefer the theatrical releases). However, I've read more than one interview with Kubrick where he makes an assertion with which I strongly disagree (and he's one of my favourite directors, so it's not like I have a negative agenda towards him). He believed viewers would be more distracted by the "black bars" than by a change in the AR of the image, so insisted there be no "black bars" on home releases (the only time OAR versions of his work have been available at home, for anything over which he held full control, has been after his death, IIRC). I used to watch my OAR widescreen VHS copy of Ben-Hur on my 13" SD TV back in the early 90s, rather than the butchered "pan and scan" version. I bought every OAR VHS release I could get my hands on, rather than the P&S versions. I reluctantly accepted P&S on VHS because so few OAR titles were available. When DVD first arrived, many films were released in "Full Screen" P&S, to placate the people who didn't like "black bars". Thankfully, that approach mostly died off in the wake of HDTVs, though the crops to 1.78 are still around, much to my chagrin (to be fair, on discs, OAR is the norm).
Few directors gave any thought to "protecting" for a different AR until TV came along. At that moment, I think it would have been best to just force people to live with the "black bars" from the get go. Viewers would have adjusted. But that genie was let out of the bottle a long time ago.
If a filmmaker chose to make something available in multiple AR, that's fine. His creation. His choices. If a third party comes along and reframes a film without the filmmaker's blessing--NOT FINE. I view that like I view colourizing a black and white film--artistic vandalism.
My beef with TUC was never that an alternate cut or AR was available--it was that, until recently, the original was not available. As long as Meyers was ok with the changes, and with the original no longer being available, I respected the limitations (though I didn't like them). Same with Star Wars--much as I prefer the original trilogy in its original form, he can do (or could until recently) whatever he wants. His creation, his rules. What I don't like is a cable movie channel just cropping/zooming a 'scope film to 1.78 to "fill the screen", with no regard to director's intent. That is heinous.