Kakashi does hit her intentionaly. what happens is she either tells kakashi or kakashi finds out she is a spy. Now here where things get tricky..When the MS is awaken the people that awakened it, in this case both kakashi and obito at the same time..they suffer short memory lost.. kakashi faints because of lack of chakra or the side effect of unlocking MS on a non uchiha or for both reasons..Obito on the other hand does not faint but goes into a short rampage and pretty much creating a bloodbath out of the bloody mist ninjas(or hidden leaf ninjas since their head band shows they might be from the leaf) This is where I figured they suffered short memory lost...Obito sees Rin on the floor dead and thinks the bloody mist killed her thats why he goes on rampage and in the current time kakashi does not know who killed rin or why her body was in the state it was meaning why did it have a hole in her chest..