I wouldn't say Kakashi doesn't stand a single chance, but how is it possible for pein to dodge the raikiri at point blank? I say rinnegan has some ability to nulify a bloodline limit.
Also this would be a good fight for Kakashi to whip out some of those 1000+ jutsu's he has.

Later on, I guess naruto, kakashi and tsunade are going to tag team pein.