Suicide? Assassination? Set-up?
I have a last theory, none of you guys thought of: the accident.
Kakashi tries to grab Rin's boob. Because of the excitement the chidori ignites from itself and Rin's whole body got pierced. Shit happens. Life goes on. Without Rin. Too bad.
Hehehe.. Luv it!
P.S. Are you guys able to find the manga reference to this! Hehehehe