Well now we're in for some drama, aren't we? This is a real problem. The rationale in both of your posts above are definitely valid. Of course, the longer he doesn't tell her, especially if it is his super-powered child, the more angry she's going to be - who knows what kind of danger a hybrid pregnancy could bring? But why would he even assume it's his? It's more rational to think Lex is the father - Clark is an alien, so why would his DNA even be compatible with a human's?
Lois has an interesting decision to make, too. Terminate the pregnancy if she believes that Lex is the father - she's not likely to want his child or disrupt her own life and career, and I fully believe that Lois is pro-choice. But if she believes it could be Clark's, if she has that "Seed of Doubt" and knows that she already loves him, she may be reluctant to terminate the pregnancy.
Or have the kid, go on TV so that Maury can say, "Lex, you ARE the father!", and sue him for child support.
to Maury!