The issue is not whether he can go against his society or not. That's been more than proven. It's about what he represents.
If the thesis of the character has been that of krypton as it is, needing to start anew, then his continued existence would counteract that.
Do you mean to imply that it's a matter of how he acts?(traditions and customs)
But Jor-El doesn't represent Krypton in any shape or form when you look at his actions. Everything he does goes against that Krypton as come to stand for.
Yes, it's all about how you act. What does it matter that he's genetically altered if it doesn't affect his actions? It's also my general view of people I meet. I don't care what race, religion, culture etc anyone belongs to. I judge people on how they act.
House El is also built around the belief that anyone can be a power for good. He apparently doesn't consider himself to be that redeemable though, despite his actions seemingly proving that he is.
But now I'm writing a bit too much again. I'll condense it to one question, to pinpoint our differences. Why exactly is it impossible for Jor-El and Lara to come and do good things on Earth? It's one of the biggest events in Superman's life so I think it's something the movie should make sure that I know.
My examples were of menacing villains that didn't start out with a perfect record and in ways were more besmirched than Zod ever was. It's speaks on the issue of how perfect a record a villain needs in order to be objectively "effective" vs what you personally find diminishes one.
It also seemed we are getting into a game of give and take. I say Scar was challenged belittled and backed down, you say his coup succeeded. Ignoring the varying difficulties of these coup attempts, the point was that if you just look for negative points to take away then they all are arguably capable of being "more effective". Like I said, how much more "effective" Voldemort would have been had the plot not needed him to fail in killing a baby in a crib. I'm sure the answer is "immensely". Doesn't mean he was ineffective, just means he could have been more so.
My point about Zod has consistently been that he never succeeds with any of his goals during the movie. The villains you brought up all manage to do some great harm, making them into big threats and therefor supporting the story arc of their respective protagonists.
A villain doesn't have to be someone that can just kick your ass, it can be someone that just schemes and deceives to get what he wants, like Scar. Scar does succeed and bends "his world" to his own rule. What else could Scar succeed with, without making the kids movie into a tragedy?
And Voldemort's situation isn't like Zod's either. Voldemort was thwarted in the past by what basically boils down to magical destiny, a common fantasy trope. Zod doesn't have anything like that, he just loses normally. Voldemort also manages to come back and take over, being seemingly unstoppable until the hero of destiny stops him. Had he been like Zod he'd never managed to defeat anyone, nor would he have managed to take over the ministry. Not that I think Harry Potter is a masterpiece of writing in it's genre.