I think it had something to do with what Obito thought was rain. Maybe it was a mist ninja jutsu that caused rin to look like the enemy.
Because in my opinion it would still be painful to be pierced by chidori.Why does she have a shocked look on her face if she saw it coming and wanted it to happen then?
nice prediction....O.Omaybe kakashi was trying to hit a mist ninja with chidori and he dogded so it hit rin instead