My reading of Lex’s worry about being a kryptonite-mutant is just psychological strain and stress. It does give us a reason for him not to start thinking about Clark as having strange powers, so that (in the future, as Sweetums suggests) he doesn’t connect Clark to the eventual Superman. He thinks that his rescues have just been lucky breaks based on his kryptonite-given power. His own ego (“it’s all about ME”) will prevent him from drawing the obvious conclusions.
In the comics, for instance, when then re-did the whole continuum, there was a bit where Luthor fed tons of data into a computer program, that told him Superman was Clark Kent. He rejected it as idiotic, because no one as powerful as Superman would take on a secret identity as meek and powerless as Clark. I thought it was a great touch, that his own ego-mania (he thinks everyone with great power would be like him) estopped him.
Of course, an interesting aside might be if Lex in SMALLVILLE really IS a kryptonite mutant, where the main effect was a super-brain… After all, the original Luthor of the comics was supposed to be super-scientist gone evil.