Depressing but intriguing turn of events
I think Luthor probably raped Lois because he might have recognized her name and it would have been a big power trip for him to violate the woman responsible for bringing down a sex scandal ring in college.
Whether the baby is his or not, L&C's reluctance for a DNA test might cause him to try to control our favorite couple (say if and when L&C find some incriminating evidence on his criminal activities)... after all he can say Lois was a virgin and her husband's probably impotent or something like that, and generally smear their reputations.
Plus whatever else might be true, Lois and Clark are still very young (1.5-2 yrs since college) and thus easy targets for the big bad people of the world.
