I did read a fic where Clark was tortured, but it had something to do with 'them' not wanting him to procreate with humans. I believe Lois and Clark were already married. Sorry, I have no idea what the name of it is.
Could be Yvonne Connell's
PurityErin Klingler's
Darkest Hour has some of the elements of your suggestion, though certainly not all of them. But is certainly worth a read, regardless.
LabRat