At first, I hated the idea, too, when it was introduced in Smallville. But did you know it was actually first introduced in the old Superboy comics? True story.
Anyway, my point is that I've grown to accept the idea of adding Luthor in Smallville to the Superman mythos. It adds to the mythos, in that it adds a bond between Clark and Lex, making their friendship more tragic when they become each other's arch-rivals. It's something that, sadly (even in Birthright), hasn't been seen to its full potential.