Poor Clark, I really feeln for him, he has to know that Chloe wouldn't think badly of him but at the same time it's probably a reflection of his own insecurities.
This really is an ingenious punishment from Jor-El.
No I think he's mainly just pissed at Oliver being a pain in the ass about it. At least it's not like canonical s8 where Oliver had such a massive stick up his ass about Clark's origins and alien shit in part cause he figured out his parents were killed over Veritas but he's not been 100% helpful yet here, at least as far as attitude goes.
Jor-el's a sadist :P