Unohana and Zaraki were fighting a very intense fight, she was bringing him to the brink of death and healing him many times to push him to his limit so that he would stop holding himself back. Eventually, he managed to overpower and stab her through the throat. There isn't necessarily a reason he killed her as we saw that he clearly didn't want her to die in Chapter 527, but the battle was a very intense clash, neither of them held back in the end, resulting in her likely death.