Isamu chose to kill Naho because Naho's troops would soon come to the two of them.
*approached Naho and held Naho's cheek*
(Isamu) "It's been one year, time feels fast, so lucky I didn't waste our time until I confessed my feelings to you"
(Naho) "Thank you, Isamu-kun, show me your right palm"
*Isamu shows his right hand to Naho and Naho makes a wound like the number 6 as proof of love for Isamu *
(Naho) "finished, it's time, Isamu-kun and please plant these Sakura seeds in my grave so I can come back to life in the form of a Sakura tree and a gust of wind"
(Isamu) "alright, it's time for me to do what you want"
*Isamu stabs Naho while kissing Naho*
Because Isamu could no longer see Naho in pain even though when Naho was stabbed she was just silent. Finally Isamu stabbed Naho several times until Naho breathed her last and died, Isamu cried, cried until he screamed. Then Isamu buried Naho's body then planted Sakura seeds according to Naho's request.
Because Isamu cried for too long at Naho's grave, Naho's troops came to arrest Isamu and then imprisoned and will be executed in the near future.