it was because they couldnt escape the ninja that were after them and because of that he had to kill her just like many ninja kill there partners so they cant be captured and intel be extracted from the person or some people like to torture there captures thats what it is...my theory is correct and to prove it do u guys remember exactly when obito saw kakashi kill rin they awakened the ms and kakashi passed out and then obito had killed all those ninja that were after kakashi and rin