I don't like to see Clark in the stressed out, overprotective mode either. But, it's easier to understand in this situation versus what occurred in say, the episode where he broke up with her "for her own good." That was just dumb!!

In this case Clark is the only one who actually knows for a fact just how close Lois came to being killed. She likely would be dead if he had not caught those bullets! I would have a hard time leaving someone I loved too; especially knowing I had the super powers to protect them.