Not sure why everyone is harping on Jor-El. He's clearly trying to protect Clark here.
SV's Darkseid seems to be some kind of ghost/demon (inspired by Satan I suppose) that manipulates people through the darkness in their hearts.
Jor-El is making Clark face his inner demons so he won't fall prey to Darkseid.
It's pretty straight forward. Though, I'm just not a fan of Clark being so screwed up all of a sudden. He seemed to be on the right track last season and this supposed internal struggle was never really played up or set up in a noteworthy way. Lois was supposed to be the person that pulled Clark from out of the darkness on the show (Pandora) but it sounds like they're stretching out that journey and making things more difficult.