Whataboutism was is a reference to your suggestion that Superman is also a war criminal. In the universe of the first movie we as the audience are essentially told by the text that Superman is good and Lex is bad. In introducing the idea that "Superman is also" as a reason to excuse teaming up with Lex seems to fit the bill for that.
As far as no true Scottsman, there's potentially a fallacy that fits better, and no true Scotsman may not even really fit the bill at all, but essentially this concept that you cannot portray someone as universally good. I just think that's not really relevant in this context and I disagree with it. I'm not saying that Superman has to be perfect. I just don't think it's good to team up with Lex. The idea that some people might not see it as a negative doesn't change the fact that some people would. And conceptually I understand that where I'd draw the line might differ from where other people draw the line, but the suggestion that where I draw the line is somehow unreasonable to the point of bringing up the idea that nobody could be perfect seems strange. I'm not suggesting that Superman is held to some high minded unrealistic standard. I think most people would agree that Lex is a bad guy and from a moralistic standpoint would prefer if Superman not have to work with him. I'm not saying it would necessarily make better media, just that we probably don't need to watch war criminals have a redemption arc at this moment in history.
Additionally, I don't care very much about what was and was not the case in the comics. My understanding is that in the comics his parents never suggested he form a harem. I think that each reboot should be considered as its own incarnation, and I think Lex in this incarnation is an objectively bad person. I do not think that the movie left any real room for interpretation there. He's not misguided, or misinformed. He's a bad guy because fundamentally at the core of his being he has these flaws that affect the way he sees the world and treats others.
Like I said, I will have to reserve ultimate judgment for when we know more about the actual content, but I just don't think it's a good premise. You seem to at least understand my subjective opinion on the matter.