But I figured it was very Lionel-esque. It has long been to his advantage to believe at one level at least that Lex had a 'dark' streak, starting with needing to believe that it was Lex that killed Julian, and running right through their relationship, justifying the necessity of manipulating Lex 'for his own good'.

I don't object to Lionel having those thoughts--as you point out, it's in his self-interest. My objection is that it is not clear to the viewer that this is Lionel being his sociopathic self here--it sounds an awful lot like something the audience is supposed to be agreeing with, as if Lionel is a reliable interpreter of Lex's actions. And for Lionel, who is the father of lies, as LaT's icon above reminds us, to suddenly become the trustworthy intepreter of Lex simply because he's now on the side of good, is what infuriated me.

And now I have to go sit for three hours in the rain at a graduation ceremony, since Californians fundamentally don't believe in rain and don't, like sensible people, make rain plans to prepare for this eventuality. I'll get to your comments when I get back.