Kakashi is not that easily defeated, but he may be badly hurt. I have a couple of theories
1. he really did get hit by the nail (he will be healed by the kages slugs) I think it will take more than 2or3 episodes to kill off a great ninja like kakashi
2. he is playing with pain its an Illusionary Techniques the Sharingan has created, from my research the Rinnegan does not protect the user from Illusionary Techniques. traits found of the rinnegan
(The Rinnegan eyes were first possessed by the founder of the ninja world and the creator of the first jutsu, the Six Realms Sage. It is characterized by a number of concentric circles around the pupil. The Rinnegan gives the user the ability to control all six types of Elemental Chakra. It's assumed that it also gives the user the ability to control rain, create copies of anyone they desire, transfer in between bodies, and gives he or she an unique array of summons. When Pain uses any number of his other bodies at a single time, he also has the power to be able to see from each of their points of view at the same time.
3. its a clone because clones have the same chakra flow so you can't tell its not the original. (IF the Rinnegan can see chakra flow)