Been desperately trying to remember the title for this fic. Lois marries Lex. Discovers he's a bad guy. Also discovers she's pregnant. Fakes her disappearance/death. Goes to the Kents' farm. Believes she killed Superman and that Clark hates her.

It sounds like it might be Sara's Made to be Broken

Or it could be "Sleeping With the Enemy" by StopQuitDont.