I've become a fan of the Batman Telltale series, so I'm going to use that an example, because there is a pretty big parallel: SPOILERS: turns out in that version, Thomas Wayne was corrupt. He got his money through the mob, he destroyed the lives of hundreds of his innocent victims, it got so bad, that even his mob allies couldn't handle working with such a monster, and had him and his wife murdered in crime alley, just to end his reign of terror. This was devastating, to Bruce, who idolized Thomas and dedicated his life to honoring his memory. But even with that new info, he didn't stop his mission to save Gotham. I liked that twist, I liked seeing Batman getting tested but staying true to his principals, and I consider Thomas Wayne's influence on Bruce Wayne to be more important than Jor-El's influence on Kal/Clark. So I'm not entirely against this Jor-El development, not conceptually anyway. My problem is actually that I think his motivation here is kinda cliche and redundant. I mean how many "humans suck, kryptonians ftw!" villains do we need?
But yeah, as far as who Superman's true dad is Jonathan Kent or Jor-El.... I mean, it's gotta be Jonathan. Jor-El is the reason he's alive, but the Kents were the ones who raised him. I think Superman absolutely should care about his kryptonian heritage and appreciate his birth parents for their sacrifice, but come on, end of the day, he doesn't even remember those people.