SN - The good of the many vs. good of the few
Possible spoilers below if you haven't watched Season 5 yet.
One continuing theme in Supernatural is the good of the many versus the good of the one. Going back to the first season, the Scarecrow episode, the villagers make human sacrifices for what they identify as the common good. You can see that Dean cannot accept this. It is very clear in Jus in Bello that Dean can't accept Ruby's spell if it will injure Nancy even if it means saving almost everyone else. Sam seems to be on the fence about accepting Ruby's offer until Dean firmly tells him no. The same theme runs through Dean's refusal to accept a role as Michael's vessel. It might save the world but too many people will be destroyed. He must look for a third way.