Regardless of whose child it is, everyone except Clark and Lois, will believe it is Clark's.
It will completely destroy the Clana ship.
The earlier concern about Sam's evil girlfriend can now be dealt with by having her be the force driving Sam to be there for his daughter.
It would be wonderful to have Clark overhear a fight between Sam and the girlfriend where she explains to him that NO MATTER WHAT LOIS IS YOUR DAUGHTER and this child, regardless of who the father is and how Lois became pregnant, WILL BE YOUR GRANDCHILD.
A scene where the girlfriend tells Lois that it may take a little time but Sam is her father and he loves her and he will love his grandchild, it may just take him sometime to get used to the idea.
Assuring her that by the time the baby is born Sam will be right there passing out
it\'s a boy or it\'s a girl candy