I wonder if whatever Clark "did" to Ellen Lane has to do with whatever happened before they "met"?
And I don't see how they can resolve their situation, given the circumstances. But on the other hand, I don't know if they really do. I mean their supposed "affair" on Regina drive doesn't mean their a "secret couple." It's a lot more likely that they just end up having sex every now and then - like what's happened so far. But, Lois at least would not be willing to have a relationship with him, even in secret.
This is probably why his parents don't know who she is. Although I'm still confused he didn't mention her back at the beginning.
Keep it coming.
Sara