Man vs Nerd or Man vs Superman?
Clark Kent is too easy to destroy.
Clark Kent doesn't threaten or look down on Luthor.
Luthor already knows that he is better than Kent even if he knows that Kent is Superman.
The only victory for a mere human being is in destroying the ubermensch.
Besides if Luthor exploits the weakness that is Clark Kent, Kal will either tidy it up bulletproof or cut it out (Superman, NO MORE!), and suddenly Superman does not have that huge chink in his armour. Allowing it to fester uncontrollably and rough is in Luthors interest.
Luthor may need to destroy Clark Kent because that facet of the Aliens personality muddies his victory of the inhuman thing from space that is subverting human will and destiny like some over bearing coddling (super) nanny.
It's like finally beating up a bully who is larger and stronger you who has been over bearing and menacing to you for years, only to discover that she has the flu quite bad and can't quite see you or form a fist at the moment you chose for the take down.