My take on the Clark/Lex conflict is that, while Clark has had multiple secret identities before, they've always been for general background research for fictional novels. He knows a lot about how the seedier side of life works, but he's never tried to bring a specific person or company down before. Along the way, he's stumbled accross enough information about Lex to know that he's dirty, but this is his first time going head-to-head with someone as sophisticated as Luthor. So, yes, he's in over his head in some aspects, and that will bite him in the butt pretty soon.
