When have we seen Vision pass out?
Again, vibranium durability feats count for Vision, because we know what material he's made of. It is the idea that Thor has the power output to 'rattle' or 'KO' vibranium, that is the part that is pure speculation, and is not supported by his previous bouts with Vibranium.
There's no doubt that Vision will be slowed down as long as Thor's lightning is on him. He may even be very uncomfortable, but if he's going to be 'injured' then that means something that is made of vibranium has to break, and nothing in the MCU has shown that kind of power. Cap No Sold Avengers Thor's strike with an inch of Vibranium. Is Post Ragnarok Thor several orders of magnitude more powerful?
Good point though on that it was the casket that was powered, but... how could the casket use that electricity to bring Vision to life without putting that electricity into him?
You do ask a good question about his abilities, but we do see him gain the durability needed to crash through many floors and no sell a flying bus, which means puts him well above Thor's feats. Then we see him use that same density manipulation to phase into and attack Ultron bots. Now, there's little thought that Thor would come apart as easily as they do, however that is an attack that Thor has no way to block.
Additionally, we see in his fight with Hawkeye that Vision's martial skill and phasing reflexes are nearly on par with world class fighter Clint Barton. So a fight with Thor would likely have exchanges rather than an instant KO, one way or the other.