I think that improving imperfections in the LaserDisc transfer, rotoscoping out scratches or dirt, for example, is completely acceptable. However, I do feel that the original effect shots, inconsistent lightsabers, matte lines, flaws and all, should definitely be preserved in an Original OT archival transfer project.

I think it's a small step into Lucas territory even when one starts fixing lightsabers. Which shots should be fixed? Should Luke's white-ish saber in the Falcon be color corrected? Should Vader's blade-less stick be painted over in the blast door closing bit? I think even if you decided to make a separate encode with these minor improvements/fixes, there would be disagreement over what should be corrected and what should be preserved the way we all remember it. Of course, it's your set...