You can't have Smallville without Lex Luthor, in the five and a half seasons so far Clarks and Lex's destinies have run parallel each others. As Rosenbaunm himself said in the Season 3 DVD Smallville has always had a ying yang to it, whatever is happening to the main character in an episode something similar is usually happening to another character, (usually Clark if the focus is not on him) examples of this are plentiful:
Ryan Clarks powers fail him, he can't save Ryan, Lex powers also fail him when he can't get a building permit from the dirty Mayor, both fail in their pursuits of other methods, the doctor Clark finds can't help Ryan, Lex puts his backing behind another candidate but a year later in Relic the seem Mayor is in power.
Redux Clark family meet problems from the past involving his Grandfather, while Lana also finds out about Henry Small for the first time
Lineage A woman confronts Clark, claiming to be his mother while Lana confronts Henry Small claiming to be his daughter
Exile While Clark is running wild in Metropolis, Lex is stranded on an island.
Precipice Both Lana and Helen are attacked by men and both Clark and Lex go above the law to deal with them.
Sometimes they have similar stories that go in the opposite direction
Rosetta Clark meets with vigil Swann and has questions answered, while Lex quest for answers is all but stopped after Dr Walden goes comatose.
[Sorry about it being season 2 heavy, I've just watched most of it recently]
Now although some of the stories that run parallel to Clark involve other characters the main stories always focus on the similar stories and how both characters react differently to them. If you look at the Season finales they are always linked together in some way;
Season 1: Both must save someone important to them, we are left wondering what Lex will do.
Season 2: Both are exiled from Smallville
Season 3: Both are "attacked" by their fathers after their betrayal, Clark is sucked into the cave and Lex is poisoned
Season 4: Both are present for the formation of stones.
Season 5: They are both locked into a battle for humanity.
To take Lex out of the show will change the fundamentals of the show and could very well change everything that is good about the show