Despite Zeke’s threats, Dean doesn't tell Cas to leave the bunker. He revels in their burgeoning relationship, content to end his day with Cas asleep on his shoulder, even if they'll always sleep in separate rooms. Cas is it for him. But when Cas begins to experience physical urges he can't control, he asks Dean for a hand—metaphorically, and later, literally.
Canon divergent after 9.03 "I'm No Angel."