American Graffiti, in my opinion, is a borderline case. Only one shot was significantly altered. It's enough (in my opinion) to bitch about, though, as it clearly separates it from the theatrical version.
Same with the CGI replacement in Raiders (the canyon shot) - if that had been the version released on DVD (it wasn't), and if that is the version released on Blu-Ray (I bet it is), I'll refuse to buy it.
But the erasing of the reflection on the glass (on the DVD) doesn't bother me enough to say it's not original. It's a bit troubling, but not that big of a deal, like the floor replacement on the Aliens Blu-Ray.