I guess I don't see the specific way Superman alters Lois' memory along the lines of gaslighting, drugging, or other said heinous acts. IMO, they're just so different, both in intent and in execution, I don't want to make the comparison. It's changing her perception of reality. I guess you can blame some of this on editing, because IIRC, in the Donner cut the solution was supposed to be going back in time and actually changing reality, but since the theatrical release of Superman the Movie already did that, Lester had to come up with a plan B. Assuming my recall is correct here, if you asked me to do a thought experiment of what was worse, changing someone's memory of what happened vs. taking away the actual experience by warping space-time, I wouldn't have an answer for you, but I could make the argument that the space-time option is potentially worse because now you affect everyone whether they like it or not.
For various reasons, I'm just not bothered by the amnesia kiss other than the fact that it's one silly aspect of a movie filled with many silly things. I understand if people disagree.
EDIT: I guess what I'm trying to say is that if someone invented a Men in Black style neuralyzer and used it wantonly on unsuspecting citizens, I might be troubled by it, but for the sake of the movie I just watch it and accept it as stuff characters in a movie do.
EDIT 2: Part of the reason I make the parallel to the time-travel and stuff is because as you say, for the sake of the movie, it's supposed to be a relatively harmless act. It doesn't become an ethical issue unless we put some heavy analysis into it and think about ramifications far beyond what the movie makers were trying to portray. I feel that kind of in-depth analysis of the amnesia kiss is required before it becomes a real ethical issue, otherwise it's just a quirky scene in a quirky movie.