i think you may be in denial here. unless supes really enjoys getting foot stomped and drug by his face his invulnerability was ....................................gone.
Kryptonite does take away his powers, even in smallville his powers go away if he's exposed to kryptonite. I remember when he took a bullet for Lois after exposure to it and it nearly killed him until he got taken outside away from the krytonite.
In the movies if supes couldn't cope with the pain then he'd fly away so that he could be away from pain, but he couldn't fly away cause kryptonite took his powers away. If you were superman and getting the crap kicked outta you and you could fly away then you would, but superman wasn't given that option due to the circumstances.
Of course his invulnerability was gone, he was getting poisoned to death. every forceful contact he receives is amplified because of the poison from the radiation.
And yes he could have fought the thugs, but he lacks the toughness of the comic book Supes.
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Iboga chose not to fight, to allow himself to evolve. He had the wisdom to abandon the actions of war when he knew they would no longer serve him.
In order for Lex Luther to be successful with the Kryptonite he would have to have all 3 of em pretty much standing in the same area. What if one of the three went closer to talk while the other 2 stood back or was lookin around. And that one dropped to the ground hed get a car thrown at him, or cut in half by heat vision Maybe even speed blitzed. Why would he even want to hurt them, he needed them to kill Supes. His persuasive skills were enough to do his bidding.. DONE