The obvious answer is to bring Clark back from the dead somehow - they never actually had a body. If he can fake healed bullet wounds somehow - with, say the help of a brilliant doctor who happens to be Lois's dad and has built cyborgs and ought to know how to convincingly fake that sort of thing - and come up with an explanation for the vanishing act it ought to be do-able.
Explaining the vanishing act is the tough part, but again a doctor or two that can be trusted might be the answer - he's been a John Doe treated for amnesia for the last few months. God knows he has a history of it...
