I'm going with your last line: "I have no idea how the writers can resolve this problem".

Is it foreshadowing that Dean was affirmed with these words: "virile manifestation of the divine"? Surely, they were funny, but in them also lies the truth. Remember it seemed that Cas and/or the leviathans did not want Michael released from Lucifer's cage. Perhaps that Dean had to break in hell, Michael had to also go to hell. Maybe (hey a girl can dream) Dean can vessel Michael and save the world.