Well It's true Jiraiya and Kakashi Were'nt in the same state when the were stabbed.
But when Jiraiya was stabbed, It stayed in his body that's what disrupted his chakra
Kakashi was stabbed for a few secconds, so it did'nt disrupt his chakra or He would'nt have been able to use that Raikiri, what must have happened was a minor "chakra sting" that was enough to throw off Kakashi's aim or else Pein would'nt have a face.
Besides Kakashi can't die, even if he were to come face-to-face with death something always comes to help him.
Enemy Assists
Zabuza = Naruto+Sasuke
Itachi = Gai
Kakuzu = Naruto
etc.
I think Kakashi can hold his own even if it will be a while, besides whose to say wat his Mangekyou will do to Pein ^_^
But if they do Kill Kakashi Than there's gonna be alot of pissed off fans
and i'm going to most likely be one of them *_*
So hurry up Naruto! lol