Oliver wants to give their relationship a chance, but Lois selflessly lets him off the hook. Later she vents her feelings to Clark:
Can you imagine what it would be like to look into somebody's eyes and know that their destiny is so much greater than yours that you will never compete, you will always be left behind?
That would be hard for anyone, but--
No, I can't be left behind one more time. You know, where Ollie's life is going, there's not room for me in it. And I know he'd never admit that, so I had to. I just, I can't face another heartbreak down the road.
In this scene, you can see Clark's concern going out to Lois. To me, the greatest aspect of the Superman mythos is Clark's love for Lois. He feels a duty to be Superman, but he also yearns, and in some tellings manages, to be there for Lois. It's this compassion that allows Lois to grow to love him.
The episode ends with Lana and Clark promising to work on trusting each other. "I don't want this to be over," Clark says.
Oh, come on! But the show is called Smallville after all.
I spoke to Lois. I'm sorry about what happened. Maybe she'll get used to the whole dual-identity thing someday.
Yeah, like when? When the earth cracks open and time ticks backwards? I don't think so.