When Bendis shipped Jon off with Crazy Grandpa Jor-El I didn't necessarily have a major problem with it because Lois was there to keep an eye on him. As Mr. Oz, he'd gone from being a mysterious dude manipulating them from the shadows to a straight up villain by the end, but the guy was also clearly being manipulated by someone else who set out to deliberately drive Jor-El crazy. I could understand where Lois & Clark were coming from in allowing Jon to go with Jor-El. Family is family after all and it would be pretty cruel to keep Jon away from his grandfather, even if he was unstable. However, when Lois decided to come back to Earth and leave Jon in the care of Jor-El, I didn't think it worked. No mother would leave their son alone with a guy shown to be as dangerous as Mr. Oz was.
But, upon re-reading The Oz Effect as part of my big Rebirth/Doomsday Clock refresh, I realised I had forgotten a very important aspect to the whole Mr. Oz/Jor-El subplot. As soon as Superman broke Mr. Oz's staff, he realised that it was controlling Jor-El's mind and his father immediately felt great sorrow for all the horrible things he'd done as Mr. Oz before being pulled away by, presumably, Dr. Manhattan. So, in the end, both Lois & Clark understood that Jor-El was not responsible for his crimes and Clark even vowed to find his father to help him.
With this in mind, when the much more sane Jor-El reappeared in Man of Steel with his offer to take Jon on a tour through the galaxy, Clark's initial wariness of his father was correct, given the last time they'd seen each other, but allowing Jon & Lois to leave with them makes much more sense. Furthermore, after spending a few days with Jor-El to ensure that he's not still being mind-controlled, Lois's decision to leave Jon with his grandfather doesn't seem as unreasonable as it did to me originally.
Finally, there's the matter of Mr. Oz's staff that was controlling him, which is uncannily similar to Rogal Zharr's staff that we're learning in Supergirl may have been influencing him. I don't believe this is a coincidence...