Take this example: in 10 years or so you decide to show Star Wars to some kids who have never seen it before. What version do you show them? The LD's have all rotted away by now. GL never did release the OT on DVD. So do you show them the Special Editions, and say, "kids, this is Star Wars", or do you show them a direct transfer like TR47's set, or do you show them your edited versions?
If you show them your edits (or GL's SE's for that matter) and say "this is Star Wars", you have showed them a lie. You have denied film history and shown them something that has no meaning. And you have changed their perception of the films. You have altered the way the next generation views the films.
There has always been fun to be had in going through the films and spotting all the dodgy effects shots. But these kids will have no such fun because you went through and airbrushed them all out. To me the films are more endearing because of the bad effects. They are a part of film legend by now.
The reason it can actually be offensive that you are doing this to the films, is every time you make a copy, you spread this version and may influence someone's perception of the films. Some kid in the future may find your version on DVD and to him or her this is what Star Wars will be. People may not know what you have done to them, and think they are direct transfers. So you are changing film history and that is why our beliefs affect what you are doing.